fix: allow nested italics inside bold spans in markdown renderer

feat(rag): pluggable RagProvider abstraction with DuckDB and Qdrant drivers

.gitignore

@@ -5,3 +5,6 @@
 .idea/
 /coyote.iml
 /.idea/
+.coyote/**
+.sisyphus/**
+.coyote-project.json

Dockerfile

@@ -36,6 +36,21 @@ RUN set -euo pipefail; \
     install -m 0755 "$TMPDIR/usql_static" /usr/local/bin/usql; \
     rm -rf "$TMPDIR"
 
+RUN set -euo pipefail; \
+    DUCKDB_VERSION=1.5.5; \
+    case "${TARGETARCH}" in \
+      amd64) DUCKDB_ARCH=amd64 ;; \
+      arm64) DUCKDB_ARCH=arm64 ;; \
+      *) echo "Unsupported TARGETARCH: ${TARGETARCH}" >&2; exit 1 ;; \
+    esac; \
+    TMPDIR=$(mktemp -d); \
+    curl -fsSL --retry 3 \
+      "https://github.com/duckdb/duckdb/releases/download/v${DUCKDB_VERSION}/duckdb_cli-linux-${DUCKDB_ARCH}.gz" \
+      -o "$TMPDIR/duckdb.gz"; \
+    gunzip "$TMPDIR/duckdb.gz"; \
+    install -m 0755 "$TMPDIR/duckdb" /usr/local/bin/duckdb; \
+    rm -rf "$TMPDIR"
+
 USER 1000
 
 RUN curl -LsSf https://astral.sh/uv/install.sh | sh && \

README.md

@@ -70,6 +70,8 @@ Coyote requires the following tools to be installed on your system:
     * **Cargo:** `cargo install ast-grep --locked`
     * **npm:** `npm i -g @ast-grep/cli`
     * Optional: if `ast-grep` is not installed, the `ast_grep` tool reports it and agents fall back to `fs_grep`
+* [duckdb](https://duckdb.org/) (for fast, local RAGs)
+    * `curl https://install.duckdb.org | sh`
 
 These tools are used to provide various functionalities within Coyote, such as document processing, JSON manipulation,
 etc., and they are used within agents and tools.

assets/functions/tools/fs_patch.sh

@@ -33,7 +33,11 @@ source "$LLM_PROMPT_UTILS_FILE"
 
 # shellcheck disable=SC2154
 main() {
-    argc_contents="$(jq -r '.content' <<< "$LLM_TOOL_RAW_JSON")"
+		# Command substitution strips *all* trailing newlines and `jq -r` appends one
+		# of its own, so read with `-j` and pin the real end of the content with a
+		# sentinel that is removed afterwards.
+		argc_contents="$(jq -j '.content' <<< "$LLM_TOOL_RAW_JSON"; printf x)"
+		argc_contents="${argc_contents%x}"
     argc_path="$(jq -r '.path' <<< "$LLM_TOOL_RAW_JSON")"
 
     if [[ ! -f "$argc_path" ]]; then
@@ -41,7 +45,11 @@ main() {
         exit 1
     fi
 
-    new_contents="$(patch_file "$argc_path" <(printf "%s" "$argc_contents"))"
+		# Same sentinel guard on the patched result, otherwise the trailing newline
+		# is stripped again on the way back out. `rc` preserves patch_file's exit
+		# status so a failure still aborts under `set -e`.
+		new_contents="$(patch_file "$argc_path" <(printf "%s" "$argc_contents"); rc=$?; printf x; exit "$rc")"
+		new_contents="${new_contents%x}"
     printf "%s" "$new_contents" | git diff --no-index "$argc_path" - || true
 
     guard_operation "Apply changes?"

assets/functions/tools/fs_write.sh

@@ -15,7 +15,12 @@ source "$LLM_PROMPT_UTILS_FILE"
 
 # shellcheck disable=SC2154
 main() {
-    argc_contents="$(jq -r '.content' <<< "$LLM_TOOL_RAW_JSON")"
+		# Command substitution strips *all* trailing newlines and `jq -r` appends one
+		# of its own, so read with `-j` and pin the real end of the content with a
+		# sentinel that is removed afterwards. Without this every written file loses
+		# its final newline, which breaks formatters such as `cargo fmt --check`.
+		argc_contents="$(jq -j '.content' <<< "$LLM_TOOL_RAW_JSON"; printf x)"
+		argc_contents="${argc_contents%x}"
     argc_path="$(jq -r '.path' <<< "$LLM_TOOL_RAW_JSON")"
 
     if [[ -f "$argc_path" ]]; then

models.yaml

@@ -841,6 +841,11 @@
       referrer: coyote
     echo_pkce_in_token_exchange: true
   models:
+    - name: grok-4.6
+      input_price: 2
+      output_price: 6
+      max_input_tokens: 500000
+      supports_function_calling: true
     - name: grok-4.5
       input_price: 2
       output_price: 6

src/cli/mod.rs

@@ -13,6 +13,20 @@ use is_terminal::IsTerminal;
 use std::collections::HashSet;
 use std::io::{Read, stdin};
 
+#[derive(clap::ValueEnum, Debug, Clone, Copy, PartialEq, Eq)]
+pub enum McpTransportArg {
+    Stdio,
+    Http,
+    Sse,
+}
+
+#[derive(clap::ValueEnum, Debug, Clone, Copy, PartialEq, Eq, Default)]
+pub enum McpScopeArg {
+    #[default]
+    User,
+    Workspace,
+}
+
 #[derive(Parser, Debug)]
 #[command(author, version, about, long_about = None)]
 #[command(
@@ -41,10 +55,15 @@ use std::io::{Read, stdin};
 				"list_skills", "skill", "tail_logs", "completions", "update",
 			])
 	),
+	group(
+		ArgGroup::new("mcp-action")
+			.args(["mcp_add", "mcp_remove", "mcp_list", "mcp_get"])
+			.multiple(false)
+	),
 )]
 pub struct Cli {
     /// Input text
-    #[arg(trailing_var_arg = true)]
+    #[arg(allow_hyphen_values = true)]
     text: Vec<String>,
 
     /// Select a LLM model
@@ -224,6 +243,57 @@ pub struct Cli {
     #[arg(long, exclusive = true, value_name = "SERVER_NAME", help_heading = "Authentication", add = ArgValueCompleter::new(mcp_server_completer))]
     pub auth_mcp: Option<String>,
 
+    /// Add an MCP server. Use `-- <cmd> [args...]` for stdio, or `--url <URL>` for http/sse.
+    #[arg(long, value_name = "NAME", help_heading = "MCP Servers")]
+    pub mcp_add: Option<String>,
+    /// Remove an MCP server by name
+    #[arg(long, value_name = "NAME", help_heading = "MCP Servers", add = ArgValueCompleter::new(mcp_server_completer))]
+    pub mcp_remove: Option<String>,
+    /// List all configured MCP servers (user + workspace scopes)
+    #[arg(long, help_heading = "MCP Servers")]
+    pub mcp_list: bool,
+    /// Show the JSON config for one MCP server
+    #[arg(long, value_name = "NAME", help_heading = "MCP Servers", add = ArgValueCompleter::new(mcp_server_completer))]
+    pub mcp_get: Option<String>,
+    /// Transport for --mcp-add: stdio (default when `--` present), http, or sse
+    #[arg(
+        long,
+        value_enum,
+        value_name = "TRANSPORT",
+        help_heading = "MCP Servers"
+    )]
+    pub transport: Option<McpTransportArg>,
+    /// URL for http/sse MCP server (used with --mcp-add)
+    #[arg(long, value_name = "URL", help_heading = "MCP Servers")]
+    pub url: Option<String>,
+    /// Scope for MCP config: user (~/.config/coyote/functions/mcp.json) or workspace (./.coyote/mcp.json). Default: user
+    #[arg(long, value_enum, value_name = "SCOPE", help_heading = "MCP Servers")]
+    pub scope: Option<McpScopeArg>,
+    /// Environment variable for stdio MCP server (repeatable): --env KEY=VALUE
+    #[arg(long, value_name = "KEY=VALUE", help_heading = "MCP Servers")]
+    pub env: Vec<String>,
+    /// HTTP header for http/sse MCP server (repeatable): --header "Name: Value"
+    #[arg(long, value_name = "HEADER", help_heading = "MCP Servers")]
+    pub header: Vec<String>,
+    /// Working directory for stdio MCP server
+    #[arg(long, value_name = "PATH", value_hint = ValueHint::AnyPath, help_heading = "MCP Servers")]
+    pub cwd: Option<String>,
+    /// OAuth client ID for http/sse MCP server
+    #[arg(long, value_name = "ID", help_heading = "MCP Servers")]
+    pub client_id: Option<String>,
+    /// OAuth client secret for http/sse MCP server (use {{NAME}} to reference a vault secret)
+    #[arg(long, value_name = "SECRET", help_heading = "MCP Servers")]
+    pub client_secret: Option<String>,
+    /// OAuth callback port for http/sse MCP server
+    #[arg(long, value_name = "PORT", help_heading = "MCP Servers")]
+    pub callback_port: Option<u16>,
+    /// OAuth redirect host for http/sse MCP server
+    #[arg(long, value_name = "HOST", help_heading = "MCP Servers")]
+    pub redirect_host: Option<String>,
+    /// Overwrite an existing MCP server (with --mcp-add) or skip confirmation (with --mcp-remove)
+    #[arg(long, help_heading = "MCP Servers")]
+    pub mcp_force: bool,
+
     /// Launch Coyote inside a Docker sandbox (via `sbx`); name defaults to current directory basename
     #[arg(long, value_name = "NAME", help_heading = "Sandbox")]
     pub sandbox: Option<Option<String>>,
@@ -254,6 +324,15 @@ pub struct Cli {
     /// Generate static shell completion scripts
     #[arg(long, value_name = "SHELL", value_enum, help_heading = "Shell")]
     pub completions: Option<ShellCompletion>,
+
+    /// Stdio command for --mcp-add: everything after `--` is passed to the server verbatim
+    #[arg(
+        last = true,
+        allow_hyphen_values = true,
+        value_name = "CMD",
+        help_heading = "MCP Servers"
+    )]
+    pub mcp_command: Vec<String>,
 }
 
 impl Cli {
@@ -633,4 +712,85 @@ mod tests {
     fn parse_sandbox_is_exclusive() {
         assert!(Cli::try_parse_from(["coyote", "--sandbox", "--agent", "foo"]).is_err());
     }
+
+    #[test]
+    fn parse_mcp_add_stdio_with_trailing_command() {
+        let cli = parse(&[
+            "--mcp-add",
+            "myserver",
+            "--",
+            "npx",
+            "some-server",
+            "--flag",
+            "arg1",
+        ]);
+        assert_eq!(cli.mcp_add, Some("myserver".to_string()));
+        assert_eq!(
+            cli.mcp_command,
+            vec!["npx", "some-server", "--flag", "arg1"]
+        );
+        assert!(cli.text.is_empty());
+    }
+
+    #[test]
+    fn parse_mcp_add_stdio_with_env_and_command() {
+        let cli = parse(&[
+            "--mcp-add",
+            "s",
+            "--env",
+            "API_KEY={{API_KEY}}",
+            "--env",
+            "MODE=dev",
+            "--",
+            "npx",
+            "srv",
+        ]);
+        assert_eq!(cli.mcp_add, Some("s".to_string()));
+        assert_eq!(cli.env, vec!["API_KEY={{API_KEY}}", "MODE=dev"]);
+        assert_eq!(cli.mcp_command, vec!["npx", "srv"]);
+    }
+
+    #[test]
+    fn parse_mcp_add_http_with_header() {
+        let cli = parse(&[
+            "--mcp-add",
+            "notion",
+            "--transport",
+            "http",
+            "--url",
+            "https://mcp.notion.com/mcp",
+            "--header",
+            "Authorization: Bearer {{NOTION_TOKEN}}",
+        ]);
+        assert_eq!(cli.mcp_add, Some("notion".to_string()));
+        assert!(matches!(cli.transport, Some(McpTransportArg::Http)));
+        assert_eq!(cli.url, Some("https://mcp.notion.com/mcp".to_string()));
+        assert_eq!(cli.header, vec!["Authorization: Bearer {{NOTION_TOKEN}}"]);
+        assert!(cli.mcp_command.is_empty());
+    }
+
+    #[test]
+    fn parse_mcp_list_flag() {
+        let cli = parse(&["--mcp-list"]);
+        assert!(cli.mcp_list);
+    }
+
+    #[test]
+    fn parse_mcp_scope_workspace() {
+        let cli = parse(&["--mcp-list", "--scope", "workspace"]);
+        assert!(cli.mcp_list);
+        assert!(matches!(cli.scope, Some(McpScopeArg::Workspace)));
+    }
+
+    #[test]
+    fn parse_mcp_action_group_is_exclusive() {
+        assert!(Cli::try_parse_from(["coyote", "--mcp-list", "--mcp-get", "foo"]).is_err());
+    }
+
+    #[test]
+    fn parse_trailing_text_unchanged_without_dash_dash() {
+        let cli = parse(&["hello", "world"]);
+        assert_eq!(cli.text, vec!["hello", "world"]);
+        assert!(cli.mcp_command.is_empty());
+    }
 }

src/client/claude.rs

@@ -1,3 +1,4 @@
+use std::collections::HashSet;
 use std::mem;
 
 use super::access_token::get_access_token;
@@ -368,17 +369,32 @@ pub fn claude_build_chat_completions_body(
                         ]
                     } else {
                         // One pair per round: Claude can reuse tool_use IDs across API calls.
+                        // A round boundary is detected by the presence of round text, but
+                        // rounds where the model emitted only tool calls (no narration)
+                        // carry no text marker. As a backstop, also split whenever a
+                        // tool_use ID would repeat within the current assistant message —
+                        // the API rejects duplicate tool_use IDs in a single message.
                         let mut messages = vec![];
                         let mut assistant_parts: Vec<serde_json::Value> = vec![];
                         let mut user_parts: Vec<serde_json::Value> = vec![];
+                        let mut chunk_ids: HashSet<&str> = HashSet::new();
                         for (index, tool_result) in tool_results.iter().enumerate() {
-                            if index > 0 && tool_result.text.is_some() {
+                            let id_collision = tool_result
+                                .call
+                                .id
+                                .as_deref()
+                                .is_some_and(|id| chunk_ids.contains(id));
+                            if index > 0 && (tool_result.text.is_some() || id_collision) {
                                 messages.push(
                                     json!({ "role": "assistant", "content": assistant_parts }),
                                 );
                                 messages.push(json!({ "role": "user", "content": user_parts }));
                                 assistant_parts = vec![];
                                 user_parts = vec![];
+                                chunk_ids.clear();
+                            }
+                            if let Some(id) = tool_result.call.id.as_deref() {
+                                chunk_ids.insert(id);
                             }
                             for block in &tool_result.thinking {
                                 assistant_parts.push(json!(block));
@@ -485,10 +501,7 @@ pub fn claude_extract_chat_completions(data: &Value) -> Result<ChatCompletionsOu
                     if let Some(v) = item["thinking"].as_str() {
                         thinking.push(ThinkingBlock::Thinking {
                             thinking: v.to_string(),
-                            signature: item["signature"]
+                            signature: item["signature"].as_str().unwrap_or_default().to_string(),
-                                .as_str()
-                                .unwrap_or_default()
-                                .to_string(),
                         });
                     }
                 }
@@ -535,3 +548,100 @@ pub fn claude_extract_chat_completions(data: &Value) -> Result<ChatCompletionsOu
     };
     Ok(output)
 }
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+    use crate::function::{ToolCall, ToolResult};
+
+    fn tool_result(id: &str, text: Option<&str>) -> ToolResult {
+        ToolResult {
+            call: ToolCall::new("fs_read".into(), json!({"path": "x"}), Some(id.into())),
+            output: json!("ok"),
+            text: text.map(|t| t.to_string()),
+            thinking: vec![],
+        }
+    }
+
+    fn build_body(tool_results: Vec<ToolResult>) -> Value {
+        let data = ChatCompletionsData {
+            messages: vec![
+                Message::new(MessageRole::User, MessageContent::Text("hello".to_string())),
+                Message::new(
+                    MessageRole::Assistant,
+                    MessageContent::ToolCalls(MessageContentToolCalls {
+                        tool_results,
+                        text: String::new(),
+                        sequence: true,
+                    }),
+                ),
+            ],
+            temperature: None,
+            top_p: None,
+            reasoning_effort: None,
+            functions: None,
+            stream: false,
+        };
+        claude_build_chat_completions_body(data, &Model::new("claude", "claude-test")).unwrap()
+    }
+
+    fn assert_unique_tool_use_ids_per_message(body: &Value) {
+        for message in body["messages"].as_array().unwrap() {
+            let Some(content) = message["content"].as_array() else {
+                continue;
+            };
+            let mut seen = HashSet::new();
+            for block in content {
+                if block["type"] == "tool_use" {
+                    let id = block["id"].as_str().unwrap();
+                    assert!(
+                        seen.insert(id.to_string()),
+                        "duplicate tool_use id `{id}` within a single assistant message: {message}"
+                    );
+                }
+            }
+        }
+    }
+
+    #[test]
+    fn sequence_splits_on_round_text() {
+        let body = build_body(vec![
+            tool_result("toolu_A", None),
+            tool_result("toolu_B", None),
+            tool_result("toolu_C", Some("running another tool")),
+        ]);
+
+        let messages = body["messages"].as_array().unwrap();
+
+        assert_eq!(messages.len(), 5, "body: {body}");
+        assert_unique_tool_use_ids_per_message(&body);
+    }
+
+    #[test]
+    fn sequence_splits_on_reused_id_in_textless_round() {
+        let body = build_body(vec![
+            tool_result("toolu_A", None),
+            tool_result("toolu_B", None),
+            tool_result("toolu_A", None),
+        ]);
+
+        let messages = body["messages"].as_array().unwrap();
+
+        assert_eq!(messages.len(), 5, "body: {body}");
+        assert_unique_tool_use_ids_per_message(&body);
+    }
+
+    #[test]
+    fn sequence_keeps_textless_rounds_merged_when_ids_are_unique() {
+        let body = build_body(vec![
+            tool_result("toolu_A", None),
+            tool_result("toolu_B", None),
+            tool_result("toolu_C", None),
+        ]);
+
+        let messages = body["messages"].as_array().unwrap();
+
+        assert_eq!(messages.len(), 3, "body: {body}");
+        assert_unique_tool_use_ids_per_message(&body);
+    }
+}

src/client/oauth.rs

@@ -2,13 +2,13 @@ use super::access_token::{is_valid_access_token, set_access_token};
 use super::openai_compatible_oauth::OpenAICompatibleOAuthProvider;
 use super::{ClientConfig, ProviderModels};
 use crate::config::paths;
-use anyhow::{Context, Result, anyhow, bail};
+use anyhow::{Context, Error, Result, anyhow, bail};
 use base64::Engine;
 use base64::engine::general_purpose::URL_SAFE_NO_PAD;
 use chrono::Utc;
 use indexmap::IndexMap;
 use inquire::Text;
-use reqwest::{Client as ReqwestClient, RequestBuilder};
+use reqwest::{Client as ReqwestClient, RequestBuilder, StatusCode};
 use serde::{Deserialize, Serialize};
 use serde_json::Value;
 use sha2::{Digest, Sha256};
@@ -16,6 +16,10 @@ use std::collections::HashMap;
 use std::fs;
 use std::io::{BufRead, BufReader, Write};
 use std::net::TcpListener;
+use std::path::PathBuf;
+use std::sync::{Arc, OnceLock};
+use std::time::Duration;
+use tokio::sync;
 use url::Url;
 use uuid::Uuid;
 
@@ -197,10 +201,20 @@ pub struct OAuthTokens {
     pub account_id: Option<String>,
 }
 
+const TOKEN_ENDPOINT_TIMEOUT: Duration = Duration::from_secs(30);
+
 pub async fn run_oauth_flow(provider: &dyn OAuthProvider, client_name: &str) -> Result<()> {
     match provider.flow() {
         OAuthFlow::Pkce => run_pkce_flow(provider, client_name).await,
-        OAuthFlow::ClientCredentials => run_client_credentials_flow(provider, client_name).await,
+        OAuthFlow::ClientCredentials => {
+            run_client_credentials_flow(provider, client_name).await?;
+            println!(
+                "Successfully authenticated client '{}' with {} via OAuth (client_credentials). Tokens saved.",
+                client_name,
+                provider.provider_name()
+            );
+            Ok(())
+        }
         OAuthFlow::DeviceCode => run_device_code_flow(provider, client_name).await,
     }
 }
@@ -301,12 +315,20 @@ async fn run_pkce_flow(provider: &dyn OAuthProvider, client_name: &str) -> Resul
 
     let access_token = response["access_token"]
         .as_str()
-        .ok_or_else(|| anyhow!("Missing access_token in response: {response}"))?
+        .ok_or_else(|| {
+            anyhow!(
+                "Missing access_token in response (keys: {})",
+                token_response_keys(&response)
+            )
+        })?
         .to_string();
     let refresh_token = response["refresh_token"].as_str().map(|s| s.to_string());
-    let expires_in = response["expires_in"]
+    let expires_in = response["expires_in"].as_i64().ok_or_else(|| {
-        .as_i64()
+        anyhow!(
-        .ok_or_else(|| anyhow!("Missing expires_in in response: {response}"))?;
+            "Missing expires_in in response (keys: {})",
+            token_response_keys(&response)
+        )
+    })?;
 
     let expires_at = Utc::now().timestamp() + expires_in;
 
@@ -334,7 +356,9 @@ async fn run_client_credentials_flow(
     provider: &dyn OAuthProvider,
     client_name: &str,
 ) -> Result<()> {
-    let client = ReqwestClient::new();
+    let client = ReqwestClient::builder()
+        .timeout(TOKEN_ENDPOINT_TIMEOUT)
+        .build()?;
     let scopes = provider.scopes();
     let mut params: Vec<(&str, &str)> = vec![
         ("grant_type", "client_credentials"),
@@ -349,11 +373,19 @@ async fn run_client_credentials_flow(
 
     let access_token = response["access_token"]
         .as_str()
-        .ok_or_else(|| anyhow!("Missing access_token in client_credentials response: {response}"))?
+        .ok_or_else(|| {
+            anyhow!(
+                "Missing access_token in client_credentials response (keys: {})",
+                token_response_keys(&response)
+            )
+        })?
         .to_string();
-    let expires_in = response["expires_in"]
+    let expires_in = response["expires_in"].as_i64().ok_or_else(|| {
-        .as_i64()
+        anyhow!(
-        .ok_or_else(|| anyhow!("Missing expires_in in client_credentials response: {response}"))?;
+            "Missing expires_in in client_credentials response (keys: {})",
+            token_response_keys(&response)
+        )
+    })?;
     let expires_at = Utc::now().timestamp() + expires_in;
 
     let tokens = OAuthTokens {
@@ -363,11 +395,6 @@ async fn run_client_credentials_flow(
         account_id: provider.extract_account_id(&response),
     };
     save_oauth_tokens(client_name, &tokens)?;
-    println!(
-        "Successfully authenticated client '{}' with {} via OAuth (client_credentials). Tokens saved.",
-        client_name,
-        provider.provider_name()
-    );
 
     Ok(())
 }
@@ -417,19 +444,28 @@ async fn run_device_code_flow(provider: &dyn OAuthProvider, client_name: &str) -
     let device_code = device_response["device_code"]
         .as_str()
         .ok_or_else(|| {
-            anyhow!("Missing device_code in device authorization response: {device_response}")
+            anyhow!(
+                "Missing device_code in device authorization response (keys: {})",
+                token_response_keys(&device_response)
+            )
         })?
         .to_string();
     let user_code = device_response["user_code"]
         .as_str()
         .ok_or_else(|| {
-            anyhow!("Missing user_code in device authorization response: {device_response}")
+            anyhow!(
+                "Missing user_code in device authorization response (keys: {})",
+                token_response_keys(&device_response)
+            )
         })?
         .to_string();
     let verification_uri = device_response["verification_uri"]
         .as_str()
         .ok_or_else(|| {
-            anyhow!("Missing verification_uri in device authorization response: {device_response}")
+            anyhow!(
+                "Missing verification_uri in device authorization response (keys: {})",
+                token_response_keys(&device_response)
+            )
         })?
         .to_string();
     let verification_uri_complete = device_response["verification_uri_complete"]
@@ -551,10 +587,76 @@ fn save_oauth_tokens(client_name: &str, tokens: &OAuthTokens) -> Result<()> {
         fs::create_dir_all(parent)?;
     }
     let json = serde_json::to_string_pretty(tokens)?;
-    fs::write(path, json)?;
+    // Write-then-rename so a crash mid-write never truncates the live token file.
+    let mut tmp = path.clone().into_os_string();
+    tmp.push(".tmp");
+    let tmp = PathBuf::from(tmp);
+    // Tokens are live credentials: create the file owner-only, not umask-default.
+    let mut options = fs::OpenOptions::new();
+    options.write(true).create(true).truncate(true);
+    #[cfg(unix)]
+    {
+        use std::os::unix::fs::OpenOptionsExt;
+        options.mode(0o600);
+    }
+    options.open(&tmp)?.write_all(json.as_bytes())?;
+    fs::rename(&tmp, &path)?;
     Ok(())
 }
 
+pub(crate) fn token_response_keys(response: &Value) -> String {
+    match response.as_object() {
+        Some(map) => {
+            let keys: Vec<&str> = map.keys().map(String::as_str).collect();
+            format!("[{}]", keys.join(", "))
+        }
+        None => "<non-object response>".to_string(),
+    }
+}
+
+fn parse_refresh_response(
+    status: StatusCode,
+    response: &Value,
+    previous_refresh_token: Option<&str>,
+) -> Result<(String, Option<String>, i64)> {
+    if let Some(error) = response["error"].as_str() {
+        let description = response["error_description"]
+            .as_str()
+            .unwrap_or("no description");
+        if matches!(error, "invalid_grant" | "invalid_token") {
+            bail!(
+                "OAuth refresh token was rejected ({error}: {description}). Please re-authenticate."
+            );
+        }
+        bail!("Token refresh failed ({error}: {description})");
+    }
+    if !status.is_success() {
+        bail!("Token refresh failed with HTTP status {status}");
+    }
+
+    let access_token = response["access_token"]
+        .as_str()
+        .ok_or_else(|| {
+            anyhow!(
+                "Missing access_token in refresh response (keys: {})",
+                token_response_keys(response)
+            )
+        })?
+        .to_string();
+    let refresh_token = response["refresh_token"]
+        .as_str()
+        .or(previous_refresh_token)
+        .map(str::to_string);
+    let expires_in = response["expires_in"].as_i64().ok_or_else(|| {
+        anyhow!(
+            "Missing expires_in in refresh response (keys: {})",
+            token_response_keys(response)
+        )
+    })?;
+
+    Ok((access_token, refresh_token, expires_in))
+}
+
 pub async fn refresh_oauth_token(
     client: &ReqwestClient,
     provider: &dyn OAuthProvider,
@@ -577,19 +679,23 @@ pub async fn refresh_oauth_token(
         ],
     );
 
-    let response: Value = request.send().await?.json().await?;
+    let (status, response) = tokio::time::timeout(TOKEN_ENDPOINT_TIMEOUT, async {
+        let response = request.send().await?;
+        let status = response.status();
+        let body: Value = response.json().await?;
+        Ok::<_, Error>((status, body))
+    })
+    .await
+    .map_err(|_| {
+        anyhow!(
+            "Token refresh for '{}' timed out after {}s",
+            client_name,
+            TOKEN_ENDPOINT_TIMEOUT.as_secs()
+        )
+    })??;
 
-    let access_token = response["access_token"]
+    let (access_token, refresh_token, expires_in) =
-        .as_str()
+        parse_refresh_response(status, &response, tokens.refresh_token.as_deref())?;
-        .ok_or_else(|| anyhow!("Missing access_token in refresh response: {response}"))?
-        .to_string();
-    let refresh_token = response["refresh_token"]
-        .as_str()
-        .map(|s| s.to_string())
-        .or_else(|| tokens.refresh_token.clone());
-    let expires_in = response["expires_in"]
-        .as_i64()
-        .ok_or_else(|| anyhow!("Missing expires_in in refresh response: {response}"))?;
 
     let expires_at = Utc::now().timestamp() + expires_in;
 
@@ -609,6 +715,20 @@ pub async fn refresh_oauth_token(
     Ok(new_tokens)
 }
 
+/// Per-client lock so concurrent requests perform a single refresh.
+/// Returns a clone of the Arc so the parking_lot guard is dropped before the
+/// caller awaits on the tokio mutex.
+fn refresh_guard(client_name: &str) -> Arc<sync::Mutex<()>> {
+    static GUARDS: OnceLock<parking_lot::Mutex<HashMap<String, Arc<sync::Mutex<()>>>>> =
+        OnceLock::new();
+    GUARDS
+        .get_or_init(Default::default)
+        .lock()
+        .entry(client_name.to_string())
+        .or_default()
+        .clone()
+}
+
 pub async fn prepare_oauth_access_token(
     client: &ReqwestClient,
     provider: &dyn OAuthProvider,
@@ -624,15 +744,35 @@ pub async fn prepare_oauth_access_token(
     };
 
     let tokens = if Utc::now().timestamp() >= tokens.expires_at {
-        match provider.flow() {
+        let guard = refresh_guard(client_name);
-            OAuthFlow::Pkce | OAuthFlow::DeviceCode => {
+        let _guard = guard.lock().await;
-                refresh_oauth_token(client, provider, client_name, &tokens).await?
+
-            }
+        // A concurrent caller may have refreshed while we waited for the
-            OAuthFlow::ClientCredentials => {
+        // lock; a valid in-memory token means the winner already populated
-                run_client_credentials_flow(provider, client_name).await?;
+        // the cache.
-                load_oauth_tokens(client_name)
+        if is_valid_access_token(client_name) {
-                    .ok_or_else(|| anyhow!("Token file missing after client_credentials refresh"))?
+            return Ok(true);
+        }
+
+        let tokens = match load_oauth_tokens(client_name) {
+            Some(t) => t,
+            None => return Ok(false),
+        };
+
+        if Utc::now().timestamp() >= tokens.expires_at {
+            match provider.flow() {
+                OAuthFlow::Pkce | OAuthFlow::DeviceCode => {
+                    refresh_oauth_token(client, provider, client_name, &tokens).await?
+                }
+                OAuthFlow::ClientCredentials => {
+                    run_client_credentials_flow(provider, client_name).await?;
+                    load_oauth_tokens(client_name).ok_or_else(|| {
+                        anyhow!("Token file missing after client_credentials refresh")
+                    })?
+                }
             }
+        } else {
+            tokens
         }
     } else {
         tokens
@@ -886,11 +1026,54 @@ pub(crate) fn client_config_info(
 
 #[cfg(test)]
 mod tests {
+    use std::ffi::OsString;
+    use std::path::PathBuf;
     use std::str;
+    use std::time::UNIX_EPOCH;
 
     use super::*;
     use crate::client::openai_compatible::OpenAICompatibleConfig;
     use crate::client::{ModelData, ProviderModels};
+    use crate::utils::get_env_name;
+    use serial_test::serial;
+    use std::{env, time::SystemTime};
+
+    fn with_temp_cache<F: FnOnce()>(f: F) {
+        struct Restore {
+            key: String,
+            prev: Option<OsString>,
+            root: PathBuf,
+        }
+        impl Drop for Restore {
+            fn drop(&mut self) {
+                unsafe {
+                    match self.prev.take() {
+                        Some(v) => env::set_var(&self.key, v),
+                        None => env::remove_var(&self.key),
+                    }
+                }
+                let _ = fs::remove_dir_all(&self.root);
+            }
+        }
+
+        let unique = SystemTime::now()
+            .duration_since(UNIX_EPOCH)
+            .unwrap()
+            .as_nanos();
+        let root = env::temp_dir().join(format!("coyote-client-oauth-test-{unique}"));
+        fs::create_dir_all(&root).unwrap();
+        let env_key = get_env_name("cache_dir");
+        let prev = env::var_os(&env_key);
+        unsafe {
+            env::set_var(&env_key, &root);
+        }
+        let _restore = Restore {
+            key: env_key,
+            prev,
+            root,
+        };
+        f();
+    }
 
     fn base_config() -> OAuthConfig {
         OAuthConfig {
@@ -1468,4 +1651,104 @@ scopes:
             "body missing grant_type param: {body}"
         );
     }
+
+    #[test]
+    #[serial]
+    fn save_oauth_tokens_roundtrips_and_leaves_no_tmp_file() {
+        with_temp_cache(|| {
+            let tokens = OAuthTokens {
+                access_token: "at-123".into(),
+                refresh_token: Some("rt-456".into()),
+                expires_at: 1234567890,
+                account_id: Some("acct-789".into()),
+            };
+
+            save_oauth_tokens("atomic-test", &tokens).unwrap();
+
+            let loaded = load_oauth_tokens("atomic-test").unwrap();
+            assert_eq!(loaded.access_token, "at-123");
+            assert_eq!(loaded.refresh_token.as_deref(), Some("rt-456"));
+            assert_eq!(loaded.expires_at, 1234567890);
+            assert_eq!(loaded.account_id.as_deref(), Some("acct-789"));
+
+            let dir = paths::oauth_tokens_dir();
+            let leftover_tmp = fs::read_dir(&dir)
+                .unwrap()
+                .any(|e| e.unwrap().file_name().to_string_lossy().ends_with(".tmp"));
+            assert!(!leftover_tmp, "temp file left behind in {dir:?}");
+
+            #[cfg(unix)]
+            {
+                use std::os::unix::fs::PermissionsExt;
+                let mode = fs::metadata(paths::token_file("atomic-test"))
+                    .unwrap()
+                    .permissions()
+                    .mode();
+                assert_eq!(mode & 0o777, 0o600, "token file mode was {mode:o}");
+            }
+        });
+    }
+
+    #[test]
+    fn parse_refresh_response_invalid_grant_redacts_and_prompts_reauth() {
+        let response = serde_json::json!({
+            "error": "invalid_grant",
+            "error_description": "refresh token revoked",
+            "refresh_token": "planted-secret-token",
+        });
+
+        let err = parse_refresh_response(StatusCode::BAD_REQUEST, &response, Some("old-rt"))
+            .unwrap_err()
+            .to_string();
+
+        assert!(err.contains("re-authenticate"), "unexpected error: {err}");
+        assert!(
+            !err.contains("planted-secret-token"),
+            "error leaked token material: {err}"
+        );
+    }
+
+    #[test]
+    fn token_response_keys_lists_keys_without_values() {
+        let response = serde_json::json!({
+            "access_token": "secret-at",
+            "token_type": "SecretBearer",
+        });
+
+        let keys = token_response_keys(&response);
+
+        assert!(keys.contains("access_token"), "missing key name: {keys}");
+        assert!(keys.contains("token_type"), "missing key name: {keys}");
+        assert!(!keys.contains("secret-at"), "leaked value: {keys}");
+        assert!(!keys.contains("SecretBearer"), "leaked value: {keys}");
+    }
+
+    #[test]
+    fn parse_refresh_response_rotates_refresh_token_when_present() {
+        let response = serde_json::json!({
+            "access_token": "new-at",
+            "refresh_token": "new-rt",
+            "expires_in": 3600,
+        });
+
+        let (access_token, refresh_token, expires_in) =
+            parse_refresh_response(StatusCode::OK, &response, Some("old-rt")).unwrap();
+
+        assert_eq!(access_token, "new-at");
+        assert_eq!(refresh_token.as_deref(), Some("new-rt"));
+        assert_eq!(expires_in, 3600);
+    }
+
+    #[test]
+    fn parse_refresh_response_keeps_old_refresh_token_when_absent() {
+        let response = serde_json::json!({
+            "access_token": "new-at",
+            "expires_in": 3600,
+        });
+
+        let (_, refresh_token, _) =
+            parse_refresh_response(StatusCode::OK, &response, Some("old-rt")).unwrap();
+
+        assert_eq!(refresh_token.as_deref(), Some("old-rt"));
+    }
 }

src/config/agent.rs

@@ -4,6 +4,7 @@ use crate::{
     client::Model,
     config::memory,
     function::{Functions, run_llm_function},
+    graph, rag,
 };
 
 use super::rag_cache::RagKey;
@@ -185,7 +186,7 @@ impl Agent {
                             &rag_path_clone,
                             &document_paths,
                             abort,
-                            false,
+                            true,
                         )
                         .await
                     })
@@ -247,6 +248,10 @@ impl Agent {
             }
         }
 
+        if rag.is_some() && app.function_calling_support && graph_for_rag.is_none() {
+            functions.append_rag_query_functions();
+        }
+
         agent_config.replace_tools_placeholder(&functions);
 
         Ok(Self {
@@ -1021,11 +1026,11 @@ async fn init_graph_rags(
             // Graph validation catches this too, but it is skipped when
             // `validate_before_run` is off, so this guard is the load-bearing one.
             if let Some(driver) = &rag_node.driver
-                && let Some(message) = crate::graph::validator::rag_driver_error(driver)
+                && let Some(message) = graph::validator::rag_driver_error(driver)
             {
                 bail!("rag node '{node_id}': {message}");
             }
-            let config = rag_init_config(rag_node);
+            let mut config = rag_init_config(rag_node);
             let fully_specified = config.embedding_model.is_some()
                 && config.chunk_size.is_some()
                 && config.chunk_overlap.is_some();
@@ -1051,6 +1056,10 @@ async fn init_graph_rags(
                          initialized. RAG initialization is required for this agent."
                     );
                 }
+
+                if config.driver.is_none() {
+                    config.driver = Some(rag::select_rag_driver()?);
+                }
             }
 
             let document_paths =

src/config/mcp_factory.rs

@@ -103,7 +103,7 @@ impl McpFactory {
         }
 
         let bearer_token = if spec.is_remote() {
-            oauth::load_valid_mcp_token(name)
+            oauth::load_or_refresh_mcp_token(name).await
         } else {
             None
         };

src/config/paths.rs

@@ -437,6 +437,10 @@ pub(crate) fn remove_rag_sidecars(dir: &Path, name: &str) -> Result<()> {
     if duckdb_path.exists() {
         let _ = remove_file(&duckdb_path);
     }
+    let wal_path = dir.join(format!("{name}.duckdb.wal"));
+    if wal_path.exists() {
+        let _ = remove_file(&wal_path);
+    }
     let mixin_path = dir.join(format!("{name}.sbx-mixin.yaml"));
     if mixin_path.exists() {
         remove_file(&mixin_path).with_context(|| {
@@ -894,16 +898,19 @@ mod tests {
     }
 
     #[test]
-    fn remove_rag_sidecars_removes_both() {
+    fn remove_rag_sidecars_removes_duckdb_wal_and_mixin() {
         let root = sidecar_temp_dir("rag-sidecars-both");
         let duckdb = root.join("docs.duckdb");
+        let wal = root.join("docs.duckdb.wal");
         let mixin = root.join("docs.sbx-mixin.yaml");
         fs::write(&duckdb, "db").unwrap();
+        fs::write(&wal, "wal").unwrap();
         fs::write(&mixin, "mixin").unwrap();
 
         remove_rag_sidecars(&root, "docs").unwrap();
 
         assert!(!duckdb.exists(), "the .duckdb sidecar must be removed");
+        assert!(!wal.exists(), "the .duckdb.wal sidecar must be removed");
         assert!(
             !mixin.exists(),
             "the .sbx-mixin.yaml sidecar must be removed"

src/config/request_context.rs

@@ -16,8 +16,9 @@ use super::{MessageContentToolCalls, prompts};
 use crate::client::{Model, ModelType, list_models};
 use crate::function::{
     FunctionDeclaration, Functions, ToolCallTracker, ToolResult, memory::MEMORY_FUNCTION_PREFIX,
-    skill::SKILL_FUNCTION_PREFIX, supervisor::SUPERVISOR_FUNCTION_PREFIX,
+    rag_query::RAG_FUNCTION_PREFIX, skill::SKILL_FUNCTION_PREFIX,
-    todo::TODO_FUNCTION_PREFIX, user_interaction::USER_FUNCTION_PREFIX,
+    supervisor::SUPERVISOR_FUNCTION_PREFIX, todo::TODO_FUNCTION_PREFIX,
+    user_interaction::USER_FUNCTION_PREFIX,
 };
 use crate::mcp::{
     MCP_DESCRIBE_META_FUNCTION_NAME_PREFIX, MCP_INVOKE_META_FUNCTION_NAME_PREFIX,
@@ -715,6 +716,7 @@ impl RequestContext {
 
     pub fn exit_rag(&mut self) -> Result<()> {
         self.rag.take();
+        self.tool_scope.functions.remove_rag_query_functions();
         Ok(())
     }
 
@@ -1137,6 +1139,7 @@ impl RequestContext {
                     && !v.name.starts_with("agent__")
                     && !v.name.starts_with("memory__")
                     && !v.name.starts_with("skill__")
+                    && !v.name.starts_with("rag__")
             })
             .map(|v| v.name.clone())
             .collect()
@@ -1957,7 +1960,8 @@ impl RequestContext {
                             || (!matches!(role.skills_enabled(), Some(false))
                                 && v.name.starts_with(SKILL_FUNCTION_PREFIX))
                             || (self.auto_continue_config().enabled
-                                && v.name.starts_with(TODO_FUNCTION_PREFIX)))
+                                && v.name.starts_with(TODO_FUNCTION_PREFIX))
+                            || v.name.starts_with(RAG_FUNCTION_PREFIX))
                             && !existing.contains(&v.name)
                     })
                     .cloned()
@@ -1987,6 +1991,7 @@ impl RequestContext {
                             || v.name.starts_with(TODO_FUNCTION_PREFIX)
                             || v.name.starts_with(SUPERVISOR_FUNCTION_PREFIX)
                             || v.name.starts_with(MEMORY_FUNCTION_PREFIX)
+                            || v.name.starts_with(RAG_FUNCTION_PREFIX)
                     });
                 }
 
@@ -3467,6 +3472,12 @@ impl RequestContext {
         if self.should_register_memory_tools() {
             functions.append_memory_functions();
         }
+        if self.rag.is_some()
+            && app.function_calling_support
+            && !self.agent.as_ref().is_some_and(|a| a.is_graph())
+        {
+            functions.append_rag_query_functions();
+        }
 
         let tool_tracker = self.tool_scope.tool_tracker.clone();
         self.tool_scope = ToolScope {
@@ -4136,7 +4147,7 @@ impl RequestContext {
                             super::TEMP_RAG_NAME,
                             &rag_path,
                             &[],
-                            abort_signal,
+                            abort_signal.clone(),
                             false,
                         )
                         .await?,
@@ -4172,10 +4183,11 @@ impl RequestContext {
         };
         self.rag = Some(rag);
         self.rag_key = rag_key;
+        self.refresh_tool_scope(abort_signal).await?;
         Ok(())
     }
 
-    pub async fn attach_rag(&mut self, name: &str) -> Result<()> {
+    pub async fn attach_rag(&mut self, name: &str, abort_signal: AbortSignal) -> Result<()> {
         let rag_path = self.rag_file(name);
         if rag_path.exists() {
             bail!(
@@ -4192,6 +4204,7 @@ impl RequestContext {
         self.rag_cache().insert(key.clone(), &rag);
         self.rag = Some(rag);
         self.rag_key = Some(key);
+        self.refresh_tool_scope(abort_signal).await?;
         Ok(())
     }
 

src/function/mod.rs

@@ -1,4 +1,5 @@
 pub(crate) mod memory;
+pub(crate) mod rag_query;
 pub(crate) mod skill;
 pub(crate) mod supervisor;
 pub(crate) mod todo;
@@ -23,6 +24,7 @@ use futures_util::future;
 use indexmap::IndexMap;
 use indoc::formatdoc;
 use memory::MEMORY_FUNCTION_PREFIX;
+use rag_query::RAG_FUNCTION_PREFIX;
 use rust_embed::Embed;
 use serde::{Deserialize, Serialize};
 use serde_json::{Value, json};
@@ -495,6 +497,16 @@ impl Functions {
             .extend(user_interaction::user_interaction_function_declarations());
     }
 
+    pub fn append_rag_query_functions(&mut self) {
+        self.declarations
+            .extend(rag_query::rag_query_function_declarations());
+    }
+
+    pub fn remove_rag_query_functions(&mut self) {
+        self.declarations
+            .retain(|f| !f.name.starts_with(RAG_FUNCTION_PREFIX));
+    }
+
     pub fn append_mcp_meta_functions(&mut self, mcp_servers: Vec<String>) {
         let mut invoke_function_properties = IndexMap::new();
         invoke_function_properties.insert(
@@ -1252,6 +1264,15 @@ impl ToolCall {
                         json!({"tool_call_error": error_msg})
                     })
             }
+            _ if cmd_name.starts_with(RAG_FUNCTION_PREFIX) => {
+                rag_query::handle_rag_tool(ctx, &cmd_name, &json_data)
+                    .await
+                    .unwrap_or_else(|e| {
+                        let error_msg = format!("RAG query failed: {e}");
+                        eprintln!("{}", muted_warning_text(&format!("⚠️ {error_msg} ⚠️")));
+                        json!({"tool_call_error": error_msg})
+                    })
+            }
             _ => match run_llm_function(cmd_name, cmd_args, envs, agent_name) {
                 Ok(Some(contents)) => serde_json::from_str(&contents)
                     .ok()

src/function/rag_query.rs

@@ -0,0 +1,101 @@
+use super::{FunctionDeclaration, JsonSchema};
+use crate::config::RequestContext;
+
+use anyhow::{Result, anyhow};
+use indexmap::IndexMap;
+use serde_json::{Value, json};
+
+pub const RAG_FUNCTION_PREFIX: &str = "rag__";
+
+pub fn rag_query_function_declarations() -> Vec<FunctionDeclaration> {
+    vec![FunctionDeclaration {
+        name: format!("{RAG_FUNCTION_PREFIX}query"),
+        description: "Search the RAG knowledge base attached to this session and return \
+                      the most relevant text chunks with their source paths. The relevant \
+                      context has already been injected into the prompt up-front; use this \
+                      tool to pull additional context on-demand when the initial retrieval \
+                      does not fully answer the question. Prefer specific, keyword-rich queries."
+            .to_string(),
+        parameters: JsonSchema {
+            type_value: Some("object".to_string()),
+            properties: Some(IndexMap::from([
+                (
+                    "query".to_string(),
+                    JsonSchema {
+                        type_value: Some("string".to_string()),
+                        description: Some(
+                            "Natural language search query used to retrieve relevant chunks."
+                                .into(),
+                        ),
+                        ..Default::default()
+                    },
+                ),
+                (
+                    "top_k".to_string(),
+                    JsonSchema {
+                        type_value: Some("integer".to_string()),
+                        description: Some(
+                            "Maximum number of chunks to return. Defaults to the RAG's \
+                             configured top_k when omitted."
+                                .into(),
+                        ),
+                        ..Default::default()
+                    },
+                ),
+            ])),
+            required: Some(vec!["query".to_string()]),
+            ..Default::default()
+        },
+        agent: false,
+    }]
+}
+
+pub async fn handle_rag_tool(
+    ctx: &mut RequestContext,
+    cmd_name: &str,
+    args: &Value,
+) -> Result<Value> {
+    let action = cmd_name
+        .strip_prefix(RAG_FUNCTION_PREFIX)
+        .unwrap_or(cmd_name);
+
+    match action {
+        "query" => handle_query(ctx, args).await,
+        _ => Err(anyhow!("Unknown RAG action: {action}")),
+    }
+}
+
+async fn handle_query(ctx: &RequestContext, args: &Value) -> Result<Value> {
+    let rag = ctx
+        .rag
+        .clone()
+        .ok_or_else(|| anyhow!("No RAG is attached to this session"))?;
+
+    let query = args
+        .get("query")
+        .and_then(Value::as_str)
+        .ok_or_else(|| anyhow!("'query' is required"))?;
+
+    let top_k = args
+        .get("top_k")
+        .and_then(Value::as_u64)
+        .map(|v| v as usize)
+        .unwrap_or_else(|| rag.configured_top_k());
+
+    let rerank_model = rag.configured_reranker().map(|s| s.to_string());
+
+    let chunks = rag
+        .search_chunks(query, top_k, rerank_model.as_deref())
+        .await?;
+
+    let chunks_json: Vec<Value> = chunks
+        .into_iter()
+        .map(|(text, source)| json!({ "text": text, "source": source }))
+        .collect();
+
+    Ok(json!({
+        "rag_name": rag.name(),
+        "count": chunks_json.len(),
+        "chunks": chunks_json,
+    }))
+}

src/main.rs

@@ -196,6 +196,18 @@ async fn main() -> Result<()> {
         return Ok(());
     }
 
+    let mcp_action =
+        cli.mcp_list || cli.mcp_get.is_some() || cli.mcp_remove.is_some() || cli.mcp_add.is_some();
+    if mcp_action {
+        let cfg = Config::load_with_interpolation(true).await?;
+        let app_config = AppConfig::from_config(cfg)?;
+        let vault = Vault::init(&app_config)?;
+
+        mcp::manage::handle(&cli, &vault)?;
+
+        return Ok(());
+    }
+
     if vault_flags {
         let cfg = Config::load_with_interpolation(true).await?;
         let app_config = AppConfig::from_config(cfg)?;

src/mcp/manage.rs

@@ -0,0 +1,443 @@
+use crate::cli::{Cli, McpScopeArg, McpTransportArg};
+use crate::config::{ensure_parent_exists, paths};
+use crate::mcp::{JsonField, McpOAuthConfig, McpServer, McpServersConfig, McpTransportType};
+use crate::vault::{SECRET_RE, Vault};
+use anyhow::{Context, Result, anyhow, bail};
+use indexmap::{IndexMap, IndexSet};
+use inquire::Confirm;
+use std::collections::HashSet;
+use std::fs;
+use std::path::{Path, PathBuf};
+
+impl From<McpTransportArg> for McpTransportType {
+    fn from(value: McpTransportArg) -> Self {
+        match value {
+            McpTransportArg::Stdio => McpTransportType::Stdio,
+            McpTransportArg::Http => McpTransportType::Http,
+            McpTransportArg::Sse => McpTransportType::Sse,
+        }
+    }
+}
+
+pub fn handle(cli: &Cli, vault: &Vault) -> Result<()> {
+    if cli.mcp_list {
+        return handle_list(cli.scope);
+    }
+    if let Some(name) = &cli.mcp_get {
+        return handle_get(name, cli.scope);
+    }
+    if let Some(name) = &cli.mcp_remove {
+        return handle_remove(name, cli.scope, cli.mcp_force);
+    }
+    if let Some(name) = &cli.mcp_add {
+        return handle_add(cli, name, vault);
+    }
+
+    Ok(())
+}
+
+fn handle_list(scope: Option<McpScopeArg>) -> Result<()> {
+    let show_user = scope != Some(McpScopeArg::Workspace);
+    let show_workspace = scope != Some(McpScopeArg::User);
+
+    if show_user {
+        let user_path = paths::mcp_config_file();
+        let user_cfg = load_config_raw(&user_path)?;
+        println!("User ({})", user_path.display());
+        print_server_list(&user_cfg);
+    }
+
+    if show_workspace {
+        match paths::workspace_mcp_config_file() {
+            Some(ws_path) => {
+                let ws_cfg = load_config_raw(&ws_path)?;
+                if show_user {
+                    println!();
+                }
+                println!("Workspace ({})", ws_path.display());
+                print_server_list(&ws_cfg);
+            }
+            None if scope == Some(McpScopeArg::Workspace) => {
+                println!("Workspace: no mcp.json found in current directory");
+            }
+            None => {}
+        }
+    }
+
+    Ok(())
+}
+
+fn print_server_list(cfg: &McpServersConfig) {
+    if cfg.mcp_servers.is_empty() {
+        println!("  (none)");
+        return;
+    }
+    let name_width = cfg.mcp_servers.keys().map(String::len).max().unwrap_or(0);
+    for (name, spec) in &cfg.mcp_servers {
+        let transport = match spec.transport_type {
+            McpTransportType::Stdio => "stdio",
+            McpTransportType::Http => "http",
+            McpTransportType::Sse => "sse",
+        };
+        let target = spec.url.clone().unwrap_or_else(|| {
+            let cmd = spec.command.clone().unwrap_or_default();
+            let args = spec.args.as_ref().map(|a| a.join(" ")).unwrap_or_default();
+            if args.is_empty() {
+                cmd
+            } else {
+                format!("{cmd} {args}")
+            }
+        });
+        println!(
+            "  {name:<name_width$}  {transport:<5}  {target}",
+            name_width = name_width
+        );
+    }
+}
+
+fn handle_get(name: &str, scope: Option<McpScopeArg>) -> Result<()> {
+    let (path, cfg) = load_for_scope_or_search(name, scope)?;
+    let spec = cfg
+        .mcp_servers
+        .get(name)
+        .ok_or_else(|| anyhow!("MCP server '{name}' not found"))?;
+    let pretty =
+        serde_json::to_string_pretty(spec).context("failed to serialize MCP server config")?;
+    println!("# {}", path.display());
+    println!("{pretty}");
+
+    Ok(())
+}
+
+fn handle_remove(name: &str, scope: Option<McpScopeArg>, force: bool) -> Result<()> {
+    let (path, mut cfg) = load_for_scope_or_search(name, scope)?;
+    if !force {
+        let ok = Confirm::new(&format!(
+            "Remove MCP server '{name}' from {}?",
+            path.display()
+        ))
+        .with_default(false)
+        .prompt()?;
+
+        if !ok {
+            println!("Aborted.");
+            return Ok(());
+        }
+    }
+
+    cfg.mcp_servers.shift_remove(name);
+    save_config(&path, &cfg)?;
+    println!("✓ Removed MCP server '{name}' from {}", path.display());
+
+    Ok(())
+}
+
+fn handle_add(cli: &Cli, name: &str, vault: &Vault) -> Result<()> {
+    validate_name(name)?;
+    let server = build_server(cli)?;
+    server.validate(name)?;
+
+    let scope = cli.scope.unwrap_or_default();
+    let path = write_path_for_scope(scope);
+    let mut cfg = load_config_raw(&path)?;
+
+    if cfg.mcp_servers.contains_key(name) && !cli.mcp_force {
+        let ok = Confirm::new(&format!(
+            "MCP server '{name}' already exists in {}. Overwrite?",
+            path.display()
+        ))
+        .with_default(false)
+        .prompt()?;
+        if !ok {
+            println!("Aborted. Use --mcp-force to overwrite without prompting.");
+            return Ok(());
+        }
+    }
+
+    provision_secrets(cli, vault)?;
+
+    cfg.mcp_servers.insert(name.to_string(), server);
+    save_config(&path, &cfg)?;
+    println!("✓ Added MCP server '{name}' to {}", path.display());
+
+    Ok(())
+}
+
+fn validate_name(name: &str) -> Result<()> {
+    if name.is_empty() {
+        bail!("MCP server name cannot be empty");
+    }
+
+    if !name
+        .chars()
+        .all(|c| c.is_ascii_alphanumeric() || c == '-' || c == '_')
+    {
+        bail!("Invalid MCP server name '{name}': only letters, digits, '-', and '_' are allowed");
+    }
+
+    Ok(())
+}
+
+fn build_server(cli: &Cli) -> Result<McpServer> {
+    let has_command = !cli.mcp_command.is_empty();
+    let has_url = cli.url.is_some();
+
+    let transport = cli
+        .transport
+        .map(McpTransportType::from)
+        .unwrap_or_else(|| {
+            if has_command {
+                McpTransportType::Stdio
+            } else {
+                McpTransportType::Http
+            }
+        });
+
+    match transport {
+        McpTransportType::Stdio => build_stdio(cli, has_url),
+        McpTransportType::Http | McpTransportType::Sse => build_remote(cli, transport, has_command),
+    }
+}
+
+fn build_stdio(cli: &Cli, has_url: bool) -> Result<McpServer> {
+    if cli.mcp_command.is_empty() {
+        bail!(
+            "stdio MCP server requires a command. Pass it after `--`, e.g. \
+             `--mcp-add NAME -- npx some-server --flag`"
+        );
+    }
+    if has_url {
+        bail!("stdio MCP server does not accept --url");
+    }
+    if !cli.header.is_empty() {
+        bail!("stdio MCP server does not accept --header");
+    }
+    if cli.client_id.is_some()
+        || cli.client_secret.is_some()
+        || cli.callback_port.is_some()
+        || cli.redirect_host.is_some()
+    {
+        bail!("stdio MCP server does not accept OAuth flags");
+    }
+
+    let (cmd, args) = cli.mcp_command.split_first().unwrap();
+
+    let mut env: IndexMap<String, JsonField> = IndexMap::new();
+    for kv in &cli.env {
+        let (k, v) = kv
+            .split_once('=')
+            .ok_or_else(|| anyhow!("invalid --env value '{kv}': expected KEY=VALUE"))?;
+        if k.is_empty() {
+            bail!("invalid --env value '{kv}': KEY cannot be empty");
+        }
+        env.insert(k.to_string(), JsonField::Str(v.to_string()));
+    }
+
+    Ok(McpServer {
+        transport_type: McpTransportType::Stdio,
+        command: Some(cmd.clone()),
+        args: (!args.is_empty()).then(|| args.to_vec()),
+        env: (!env.is_empty()).then_some(env),
+        cwd: cli.cwd.clone(),
+        url: None,
+        headers: None,
+        oauth: None,
+    })
+}
+
+fn build_remote(cli: &Cli, transport: McpTransportType, has_command: bool) -> Result<McpServer> {
+    if has_command {
+        bail!(
+            "http/sse MCP server does not accept a trailing `-- <cmd>`. Use `--url` \
+             to specify the endpoint."
+        );
+    }
+    let url = cli
+        .url
+        .clone()
+        .ok_or_else(|| anyhow!("http/sse MCP server requires --url <URL>"))?;
+    if !cli.env.is_empty() {
+        bail!("http/sse MCP server does not accept --env; use --header instead");
+    }
+    if cli.cwd.is_some() {
+        bail!("http/sse MCP server does not accept --cwd");
+    }
+
+    let mut headers: IndexMap<String, String> = IndexMap::new();
+    for h in &cli.header {
+        let (name, value) = h
+            .split_once(':')
+            .ok_or_else(|| anyhow!("invalid --header value '{h}': expected 'Name: Value'"))?;
+        let name = name.trim();
+        let value = value.trim_start_matches(' ');
+        if name.is_empty() {
+            bail!("invalid --header value '{h}': header name cannot be empty");
+        }
+        headers.insert(name.to_string(), value.to_string());
+    }
+
+    let oauth = if cli.client_id.is_some()
+        || cli.client_secret.is_some()
+        || cli.callback_port.is_some()
+        || cli.redirect_host.is_some()
+    {
+        Some(McpOAuthConfig {
+            client_id: cli.client_id.clone(),
+            client_secret: cli.client_secret.clone(),
+            callback_port: cli.callback_port,
+            redirect_host: cli.redirect_host.clone(),
+        })
+    } else {
+        None
+    };
+
+    Ok(McpServer {
+        transport_type: transport,
+        command: None,
+        args: None,
+        env: None,
+        cwd: None,
+        url: Some(url),
+        headers: (!headers.is_empty()).then_some(headers),
+        oauth,
+    })
+}
+
+fn provision_secrets(cli: &Cli, vault: &Vault) -> Result<()> {
+    let mut sources: Vec<&str> = Vec::new();
+    if let Some(s) = cli.url.as_deref() {
+        sources.push(s);
+    }
+    if let Some(s) = cli.client_secret.as_deref() {
+        sources.push(s);
+    }
+    if let Some(s) = cli.client_id.as_deref() {
+        sources.push(s);
+    }
+    if let Some(s) = cli.redirect_host.as_deref() {
+        sources.push(s);
+    }
+    if let Some(s) = cli.cwd.as_deref() {
+        sources.push(s);
+    }
+    sources.extend(cli.env.iter().map(String::as_str));
+    sources.extend(cli.header.iter().map(String::as_str));
+
+    let mut needed: IndexSet<String> = IndexSet::new();
+    for value in sources {
+        for caps in SECRET_RE.captures_iter(value).filter_map(Result::ok) {
+            if let Some(m) = caps.get(1) {
+                needed.insert(m.as_str().trim().to_string());
+            }
+        }
+    }
+
+    if needed.is_empty() {
+        return Ok(());
+    }
+
+    let existing: HashSet<String> = vault.list_secrets(false)?.into_iter().collect();
+    for name in needed {
+        if existing.contains(&name) {
+            continue;
+        }
+        eprintln!("Value references vault secret {{{{ {name} }}}} which is not stored yet.");
+        let ok = Confirm::new(&format!("Add '{name}' to the vault now?"))
+            .with_default(true)
+            .prompt()?;
+        if !ok {
+            bail!(
+                "Vault secret '{name}' is required by the config; aborting. \
+                 Add it later with `coyote --add-secret {name}`."
+            );
+        }
+        vault.add_secret(&name)?;
+    }
+
+    Ok(())
+}
+
+fn load_for_scope_or_search(
+    name: &str,
+    scope: Option<McpScopeArg>,
+) -> Result<(PathBuf, McpServersConfig)> {
+    if let Some(s) = scope {
+        let path = match s {
+            McpScopeArg::User => paths::mcp_config_file(),
+            McpScopeArg::Workspace => paths::workspace_mcp_config_file()
+                .ok_or_else(|| anyhow!("no workspace mcp.json found in the current directory"))?,
+        };
+        let cfg = load_config_raw(&path)?;
+        if !cfg.mcp_servers.contains_key(name) {
+            bail!(
+                "MCP server '{name}' not found in {} scope ({})",
+                scope_label(s),
+                path.display()
+            );
+        }
+
+        return Ok((path, cfg));
+    }
+
+    let user_path = paths::mcp_config_file();
+    let user_cfg = load_config_raw(&user_path)?;
+    if user_cfg.mcp_servers.contains_key(name) {
+        return Ok((user_path, user_cfg));
+    }
+
+    if let Some(ws_path) = paths::workspace_mcp_config_file() {
+        let ws_cfg = load_config_raw(&ws_path)?;
+        if ws_cfg.mcp_servers.contains_key(name) {
+            return Ok((ws_path, ws_cfg));
+        }
+    }
+
+    bail!("MCP server '{name}' not found in any scope");
+}
+
+fn write_path_for_scope(scope: McpScopeArg) -> PathBuf {
+    match scope {
+        McpScopeArg::User => paths::mcp_config_file(),
+        McpScopeArg::Workspace => paths::workspace_mcp_config_file()
+            .unwrap_or_else(|| paths::workspace_config_dir().join("mcp.json")),
+    }
+}
+
+fn scope_label(scope: McpScopeArg) -> &'static str {
+    match scope {
+        McpScopeArg::User => "user",
+        McpScopeArg::Workspace => "workspace",
+    }
+}
+
+fn load_config_raw(path: &Path) -> Result<McpServersConfig> {
+    if !path.exists() {
+        return Ok(McpServersConfig {
+            mcp_servers: IndexMap::new(),
+        });
+    }
+
+    let raw = fs::read_to_string(path)
+        .with_context(|| format!("failed to read MCP config at {}", path.display()))?;
+    if raw.trim().is_empty() {
+        return Ok(McpServersConfig {
+            mcp_servers: IndexMap::new(),
+        });
+    }
+
+    serde_json::from_str(&raw)
+        .with_context(|| format!("failed to parse MCP config at {}", path.display()))
+}
+
+fn save_config(path: &Path, config: &McpServersConfig) -> Result<()> {
+    ensure_parent_exists(path)?;
+    let serialized =
+        serde_json::to_string_pretty(config).context("failed to serialize MCP config")?;
+    let tmp = path.with_extension("json.tmp");
+    fs::write(&tmp, &serialized)
+        .with_context(|| format!("failed to write temporary MCP config at {}", tmp.display()))?;
+    fs::rename(&tmp, path)
+        .with_context(|| format!("failed to finalize MCP config at {}", path.display()))?;
+
+    Ok(())
+}

src/mcp/mod.rs

@@ -1,3 +1,4 @@
+pub(crate) mod manage;
 pub(crate) mod oauth;
 mod sse_transport;
 
@@ -62,6 +63,8 @@ pub(crate) struct McpServersConfig {
 pub(crate) struct McpOAuthConfig {
     #[serde(rename = "clientId", skip_serializing_if = "Option::is_none")]
     pub client_id: Option<String>,
+    #[serde(rename = "clientSecret", skip_serializing_if = "Option::is_none")]
+    pub client_secret: Option<String>,
     #[serde(rename = "callbackPort", skip_serializing_if = "Option::is_none")]
     pub callback_port: Option<u16>,
     #[serde(rename = "redirectHost", skip_serializing_if = "Option::is_none")]
@@ -324,7 +327,7 @@ impl McpRegistry {
             .with_context(|| format!("MCP server not found in config: {id}"))?;
 
         let bearer_token = if spec.is_remote() {
-            oauth::load_valid_mcp_token(&id)
+            oauth::load_or_refresh_mcp_token(&id).await
         } else {
             None
         };

src/mcp/oauth.rs

@@ -1,15 +1,25 @@
-use crate::client::oauth::{OAuthProvider, TokenRequestFormat, load_oauth_tokens, run_oauth_flow};
+use crate::client::oauth::{
+    OAuthProvider, OAuthTokens, TokenRequestFormat, load_oauth_tokens, refresh_oauth_token,
+    run_oauth_flow, token_response_keys,
+};
 use crate::config::paths;
 use anyhow::{Context, Result, anyhow};
 use chrono::Utc;
 use inquire::Text;
-use log::warn;
+use log::{debug, warn};
 use reqwest::Client;
 use serde::{Deserialize, Serialize};
+use std::collections::HashMap;
 use std::fs;
 use std::net::TcpListener;
+use std::sync::{Arc, OnceLock};
+use std::time::{Duration, Instant};
+use tokio::sync;
 use url::Url;
 
+const REFRESH_HTTP_TIMEOUT: Duration = Duration::from_secs(10);
+const REFRESH_FAILURE_BACKOFF: Duration = Duration::from_secs(60);
+
 #[derive(Debug, Deserialize)]
 struct ProtectedResourceMetadata {
     #[serde(default)]
@@ -34,6 +44,10 @@ struct McpRegistration {
     client_id: String,
     #[serde(default)]
     redirect_uri: Option<String>,
+    #[serde(default)]
+    token_url: Option<String>,
+    #[serde(default)]
+    resource: Option<String>,
 }
 
 struct DiscoveredOAuth {
@@ -124,8 +138,19 @@ pub async fn run_mcp_oauth_flow(
         None
     };
 
-    let (client_id, redirect_uri) = if let Some(reused) = cached_reuse {
+    let (client_id, redirect_uri) = if let Some((client_id, redirect_uri)) = cached_reuse {
-        reused
+        // Re-save so registrations cached before token_url/resource were
+        // persisted gain them, enabling token refresh next time.
+        if let Err(e) = save_registration(
+            server_name,
+            &client_id,
+            &redirect_uri,
+            &metadata.token_endpoint,
+            &resource,
+        ) {
+            debug!("Failed to update cached MCP registration for '{server_name}': {e}");
+        }
+        (client_id, redirect_uri)
     } else {
         let bind_addr = format!("127.0.0.1:{}", callback_port.unwrap_or(0));
         let listener = TcpListener::bind(&bind_addr)?;
@@ -137,10 +162,7 @@ pub async fn run_mcp_oauth_flow(
             id.to_string()
         } else if let Some(reg_endpoint) = &metadata.registration_endpoint {
             match register_client(reg_endpoint, &redirect_uri).await {
-                Ok(id) => {
+                Ok(id) => id,
-                    let _ = save_registration(server_name, &id, &redirect_uri);
-                    id
-                }
                 Err(e) => {
                     warn!("Dynamic client registration failed: {e}. Falling back to manual entry.");
                     Text::new("Enter the OAuth client ID for this MCP server:")
@@ -153,6 +175,18 @@ pub async fn run_mcp_oauth_flow(
                 .prompt()
                 .context("Failed to read client ID")?
         };
+        // Persist regardless of how the client_id was obtained (DCR, config,
+        // or manual entry) so refresh_mcp_token can run the refresh_token
+        // grant later without interactive re-auth.
+        if let Err(e) = save_registration(
+            server_name,
+            &client_id,
+            &redirect_uri,
+            &metadata.token_endpoint,
+            &resource,
+        ) {
+            debug!("Failed to cache MCP registration for '{server_name}': {e}");
+        }
         (client_id, redirect_uri)
     };
 
@@ -168,12 +202,113 @@ pub async fn run_mcp_oauth_flow(
     run_oauth_flow(&provider, &mcp_token_key(server_name)).await
 }
 
-pub fn load_valid_mcp_token(server_name: &str) -> Option<String> {
+pub async fn load_or_refresh_mcp_token(server_name: &str) -> Option<String> {
-    let tokens = load_oauth_tokens(&mcp_token_key(server_name))?;
+    let key = mcp_token_key(server_name);
+    let tokens = load_oauth_tokens(&key)?;
     if Utc::now().timestamp() < tokens.expires_at {
-        Some(tokens.access_token)
+        return Some(tokens.access_token);
-    } else {
+    }
-        None
+
+    if in_refresh_failure_backoff(server_name) {
+        debug!("Skipping token refresh for MCP server '{server_name}': recent attempt failed");
+        return None;
+    }
+
+    let lock = refresh_lock(server_name);
+    let _guard = lock.lock().await;
+
+    // A concurrent caller may have refreshed while we waited for the lock.
+    let tokens = load_oauth_tokens(&key)?;
+    if Utc::now().timestamp() < tokens.expires_at {
+        return Some(tokens.access_token);
+    }
+
+    if in_refresh_failure_backoff(server_name) {
+        debug!("Skipping token refresh for MCP server '{server_name}': recent attempt failed");
+        return None;
+    }
+
+    match refresh_mcp_token(server_name, &key, &tokens).await {
+        Ok(access_token) => Some(access_token),
+        Err(e) => {
+            note_refresh_failure(server_name);
+            warn!(
+                "Failed to refresh OAuth token for MCP server '{server_name}'. \
+                 Run `.mcp auth {server_name}` to re-authenticate."
+            );
+            debug!(
+                "Token refresh error for MCP server '{server_name}': {}",
+                redact_refresh_error(&e)
+            );
+            None
+        }
+    }
+}
+
+async fn refresh_mcp_token(server_name: &str, key: &str, tokens: &OAuthTokens) -> Result<String> {
+    if tokens.refresh_token.is_none() {
+        return Err(anyhow!("no refresh token stored"));
+    }
+
+    let reg =
+        load_registration(server_name).ok_or_else(|| anyhow!("no cached client registration"))?;
+    let token_url = reg.token_url.ok_or_else(|| {
+        anyhow!("cached registration has no token URL (saved by an older version)")
+    })?;
+    let resource = reg.resource.ok_or_else(|| {
+        anyhow!("cached registration has no resource (saved by an older version)")
+    })?;
+
+    let provider = McpOAuthProvider {
+        client_id: reg.client_id,
+        authorize_url: String::new(),
+        token_url,
+        scopes: String::new(),
+        fixed_redirect: String::new(),
+        resource,
+    };
+
+    let client = Client::builder().timeout(REFRESH_HTTP_TIMEOUT).build()?;
+    let refreshed = refresh_oauth_token(&client, &provider, key, tokens).await?;
+    Ok(refreshed.access_token)
+}
+
+fn refresh_lock(server_name: &str) -> Arc<sync::Mutex<()>> {
+    static LOCKS: OnceLock<parking_lot::Mutex<HashMap<String, Arc<sync::Mutex<()>>>>> =
+        OnceLock::new();
+    LOCKS
+        .get_or_init(Default::default)
+        .lock()
+        .entry(server_name.to_string())
+        .or_default()
+        .clone()
+}
+
+fn refresh_failures() -> &'static parking_lot::Mutex<HashMap<String, Instant>> {
+    static FAILURES: OnceLock<parking_lot::Mutex<HashMap<String, Instant>>> = OnceLock::new();
+    FAILURES.get_or_init(Default::default)
+}
+
+fn note_refresh_failure(server_name: &str) {
+    refresh_failures()
+        .lock()
+        .insert(server_name.to_string(), Instant::now());
+}
+
+fn in_refresh_failure_backoff(server_name: &str) -> bool {
+    refresh_failures()
+        .lock()
+        .get(server_name)
+        .is_some_and(|failed_at| failed_at.elapsed() < REFRESH_FAILURE_BACKOFF)
+}
+
+/// Refresh errors may embed the token endpoint's JSON response, which can
+/// contain live tokens; strip everything from the first `{` before logging.
+fn redact_refresh_error(e: &anyhow::Error) -> String {
+    let msg = e.to_string();
+    match msg.find('{') {
+        Some(idx) => format!("{}<response body redacted>", &msg[..idx]),
+        None => msg,
     }
 }
 
@@ -187,7 +322,13 @@ fn load_registration(server_name: &str) -> Option<McpRegistration> {
     serde_json::from_str(&content).ok()
 }
 
-fn save_registration(server_name: &str, client_id: &str, redirect_uri: &str) -> Result<()> {
+fn save_registration(
+    server_name: &str,
+    client_id: &str,
+    redirect_uri: &str,
+    token_url: &str,
+    resource: &str,
+) -> Result<()> {
     let dir = paths::oauth_tokens_dir();
     fs::create_dir_all(&dir)?;
 
@@ -195,6 +336,8 @@ fn save_registration(server_name: &str, client_id: &str, redirect_uri: &str) ->
     let reg = McpRegistration {
         client_id: client_id.to_string(),
         redirect_uri: Some(redirect_uri.to_string()),
+        token_url: Some(token_url.to_string()),
+        resource: Some(resource.to_string()),
     };
 
     fs::write(path, serde_json::to_string_pretty(&reg)?)?;
@@ -244,7 +387,12 @@ async fn register_client(endpoint: &str, redirect_uri: &str) -> Result<String> {
 
     response["client_id"]
         .as_str()
-        .ok_or_else(|| anyhow!("Missing client_id in registration response: {response}"))
+        .ok_or_else(|| {
+            anyhow!(
+                "Missing client_id in registration response (keys: {})",
+                token_response_keys(&response)
+            )
+        })
         .map(|s| s.to_string())
 }
 
@@ -426,11 +574,31 @@ mod tests {
     use crate::utils::get_env_name;
     use serial_test::serial;
     use std::{
-        env, fs,
+        env,
+        ffi::OsString,
+        fs,
+        path::PathBuf,
         time::{self, SystemTime},
     };
 
     fn with_temp_cache<F: FnOnce()>(f: F) {
+        struct Restore {
+            key: String,
+            prev: Option<OsString>,
+            root: PathBuf,
+        }
+        impl Drop for Restore {
+            fn drop(&mut self) {
+                unsafe {
+                    match self.prev.take() {
+                        Some(v) => env::set_var(&self.key, v),
+                        None => env::remove_var(&self.key),
+                    }
+                }
+                let _ = fs::remove_dir_all(&self.root);
+            }
+        }
+
         let unique = SystemTime::now()
             .duration_since(time::UNIX_EPOCH)
             .unwrap()
@@ -442,14 +610,12 @@ mod tests {
         unsafe {
             env::set_var(&env_key, &root);
         }
+        let _restore = Restore {
+            key: env_key,
+            prev,
+            root,
+        };
         f();
-        unsafe {
-            match prev {
-                Some(v) => env::set_var(&env_key, v),
-                None => env::remove_var(&env_key),
-            }
-        }
-        let _ = fs::remove_dir_all(&root);
     }
 
     #[test]
@@ -685,12 +851,19 @@ mod tests {
                 "notion",
                 "client-xyz-123",
                 "http://127.0.0.1:49152/callback",
+                "https://as.example/token",
+                "https://mcp.example/mcp",
             )
             .unwrap();
 
-            let loaded = load_registration("notion");
+            let loaded = load_registration("notion").unwrap();
 
-            assert_eq!(loaded.unwrap().client_id, "client-xyz-123");
+            assert_eq!(loaded.client_id, "client-xyz-123");
+            assert_eq!(
+                loaded.token_url.as_deref(),
+                Some("https://as.example/token")
+            );
+            assert_eq!(loaded.resource.as_deref(), Some("https://mcp.example/mcp"));
         });
     }
 
@@ -708,8 +881,22 @@ mod tests {
     #[serial]
     fn registration_second_save_overwrites_first() {
         with_temp_cache(|| {
-            save_registration("github", "first-id", "http://127.0.0.1:49152/callback").unwrap();
+            save_registration(
-            save_registration("github", "second-id", "http://127.0.0.1:49153/callback").unwrap();
+                "github",
+                "first-id",
+                "http://127.0.0.1:49152/callback",
+                "https://as.example/token",
+                "https://mcp.example/mcp",
+            )
+            .unwrap();
+            save_registration(
+                "github",
+                "second-id",
+                "http://127.0.0.1:49153/callback",
+                "https://as.example/token",
+                "https://mcp.example/mcp",
+            )
+            .unwrap();
 
             let loaded = load_registration("github").unwrap();
 
@@ -737,6 +924,8 @@ mod tests {
 
             assert_eq!(loaded.client_id, "legacy-id");
             assert_eq!(loaded.redirect_uri, None);
+            assert_eq!(loaded.token_url, None);
+            assert_eq!(loaded.resource, None);
         });
     }
 
@@ -744,7 +933,14 @@ mod tests {
     #[serial]
     fn save_registration_persists_redirect_uri() {
         with_temp_cache(|| {
-            save_registration("aws", "client-abc", "http://127.0.0.1:49152/callback").unwrap();
+            save_registration(
+                "aws",
+                "client-abc",
+                "http://127.0.0.1:49152/callback",
+                "https://as.example/token",
+                "https://mcp.example/mcp",
+            )
+            .unwrap();
 
             let loaded = load_registration("aws").unwrap();
 
@@ -756,6 +952,82 @@ mod tests {
         });
     }
 
+    #[test]
+    fn mcp_registration_deserializes_without_new_fields_and_roundtrips() {
+        let old: McpRegistration = serde_json::from_str(r#"{"client_id":"legacy-id"}"#).unwrap();
+
+        assert_eq!(old.client_id, "legacy-id");
+        assert_eq!(old.token_url, None);
+        assert_eq!(old.resource, None);
+
+        let full = McpRegistration {
+            client_id: "client-abc".into(),
+            redirect_uri: Some("http://127.0.0.1:49152/callback".into()),
+            token_url: Some("https://as.example/token".into()),
+            resource: Some("https://mcp.example/mcp".into()),
+        };
+        let json = serde_json::to_string(&full).unwrap();
+        let back: McpRegistration = serde_json::from_str(&json).unwrap();
+
+        assert_eq!(back.token_url.as_deref(), Some("https://as.example/token"));
+        assert_eq!(back.resource.as_deref(), Some("https://mcp.example/mcp"));
+    }
+
+    #[test]
+    #[serial]
+    fn expired_token_with_old_format_registration_returns_none() {
+        with_temp_cache(|| {
+            let dir = paths::oauth_tokens_dir();
+            fs::create_dir_all(&dir).unwrap();
+            fs::write(
+                paths::token_file("mcp_legacyref"),
+                r#"{"access_token":"stale","refresh_token":"refresh-abc","expires_at":0}"#,
+            )
+            .unwrap();
+            fs::write(
+                dir.join("mcp_legacyref_registration.json"),
+                r#"{"client_id":"legacy-id"}"#,
+            )
+            .unwrap();
+
+            let rt = tokio::runtime::Builder::new_current_thread()
+                .enable_all()
+                .build()
+                .unwrap();
+            let token = rt.block_on(load_or_refresh_mcp_token("legacyref"));
+
+            assert_eq!(token, None);
+        });
+    }
+
+    #[test]
+    fn refresh_failure_backoff_memoizes_per_server() {
+        assert!(!in_refresh_failure_backoff("backoff-test-server"));
+
+        note_refresh_failure("backoff-test-server");
+
+        assert!(in_refresh_failure_backoff("backoff-test-server"));
+        assert!(!in_refresh_failure_backoff("backoff-other-server"));
+    }
+
+    #[test]
+    fn redact_refresh_error_strips_response_body() {
+        let with_body = anyhow!(
+            "Missing access_token in refresh response: {}",
+            r#"{"access_token":"live-secret"}"#
+        );
+        let without_body = anyhow!("no refresh token stored");
+
+        assert_eq!(
+            redact_refresh_error(&with_body),
+            "Missing access_token in refresh response: <response body redacted>"
+        );
+        assert_eq!(
+            redact_refresh_error(&without_body),
+            "no refresh token stored"
+        );
+    }
+
     #[test]
     fn cached_redirect_port_matches() {
         let port = cached_redirect_port("http://127.0.0.1:49152/callback", "127.0.0.1", None);

src/rag/mod.rs

@@ -267,31 +267,10 @@ impl Rag {
         }
         println!("⚙ Initializing RAG...");
         let (embedding_model, chunk_size, chunk_overlap) = Self::create_config(app)?;
-        // Only interactive named-RAG creation offers a driver choice. Temp RAGs and
-        // agent startup pass `false`; an explicit flag is used rather than inferring
-        // from the name because the agent path passes the literal name "rag", which is
-        // indistinguishable from a user creating a RAG genuinely named `rag`.
         let driver = if prompt_for_driver {
-            let options = vec![
+            select_rag_driver()?
-                "yaml   — portable, in-memory HNSW; usable from several Coyote processes at once (default)",
-                "duckdb — persistent on-disk store; vectors and content survive restarts; HNSW approximate search.",
-            ];
-            let sel = Select::new("RAG storage driver:", options)
-                .with_starting_cursor(0)
-                .prompt()?;
-            if sel.starts_with("duckdb") {
-                println!(
-                    "Note: several Coyote processes can query a duckdb RAG at the same time, \
-                     but while one process is ingesting or rebuilding it the others cannot \
-                     read it until that finishes. Changing its driver later means deleting \
-                     and recreating the RAG."
-                );
-                "duckdb"
-            } else {
-                "yaml"
-            }
         } else {
-            "yaml"
+            "yaml".to_string()
         };
         let reranker_model = app.rag_reranker_model.clone();
         let top_k = app.rag_top_k;
@@ -318,7 +297,7 @@ impl Rag {
                 graph_hops: Some(graph_hops),
             },
         );
-        data.driver = driver.to_string();
+        data.driver = driver;
         let mut rag = Self::create(app, name, save_path, data)?;
         let mut paths = doc_paths.to_vec();
         if paths.is_empty() {
@@ -586,19 +565,40 @@ impl Rag {
                 if data.vectors.is_empty() {
                     data.vectors = duck.read_all_vectors()?;
                 }
+                if data.vectors.is_empty() && !data.files.is_empty() {
+                    println!(
+                        "{} RAG '{name}' lists {} indexed file(s), but its vector store \
+                         '{}' holds no vectors, so every search will return nothing. A \
+                         duckdb RAG is two files: bring the .duckdb sidecar along with \
+                         the .yaml, or re-embed with `.rebuild rag`.",
+                        warning_text("WARNING:"),
+                        data.files.len(),
+                        db_path.display()
+                    );
+                }
                 // data.files is always populated for duckdb, so build_bm25() is the only
                 // path; there is no from-DuckDB fallback.
                 let bm25 = data.build_bm25();
                 (Box::new(duck), bm25)
             }
             "qdrant" => bail!(
-                "Qdrant RAGs cannot be constructed via Rag::create(); \
+                "RAG '{name}' uses driver 'qdrant' without `attached: true`. \
-                 use Rag::attach() or Rag::load_async() instead"
+                 Coyote can currently only READ a pre-existing Qdrant \
+                 collection — attach one with `.rag attach`. Writing to a \
+                 Coyote-owned Qdrant collection is not supported yet."
             ),
-            _ => {
+            "yaml" => {
                 let bm25 = data.build_bm25();
                 (Box::new(YamlProvider::from_data(&data)), bm25)
             }
+            // Explicitly NOT a catch-all falling through to yaml. A typo'd driver
+            // used to build a yaml store, pay to embed the whole corpus, persist
+            // the bad driver, and only fail on the NEXT run, leaving the RAG
+            // unusable without hand-editing the YAML.
+            other => bail!(
+                "Unknown RAG driver '{other}' for RAG '{name}'. \
+                 Valid drivers: yaml, duckdb, qdrant."
+            ),
         };
         let node_to_docs = data.knowledge_graph.build_node_to_docs();
         let embedding_model =
@@ -856,6 +856,20 @@ impl Rag {
         Ok((embeddings, sources, ids))
     }
 
+    pub async fn search_chunks(
+        &self,
+        text: &str,
+        top_k: usize,
+        rerank_model: Option<&str>,
+    ) -> Result<Vec<(String, String)>> {
+        let results = self.hybrid_search(text, top_k, rerank_model).await?;
+
+        Ok(results
+            .into_iter()
+            .map(|(id, content)| (content, self.resolve_source(&id)))
+            .collect())
+    }
+
     pub async fn search_with_template(
         &self,
         app: &AppConfig,
@@ -1169,12 +1183,7 @@ impl Rag {
         top_k: usize,
         rerank_model: Option<&str>,
     ) -> Result<Vec<(DocumentId, String)>> {
-        let vector_search_results = self.vector_search(query, top_k, 0.0).await?;
+        let keyword_leg = async {
-        debug!("vector_search_results: {vector_search_results:?}",);
-        let vector_search_ids: Vec<DocumentId> =
-            vector_search_results.into_iter().map(|(v, _)| v).collect();
-
-        let keyword_search_results: Vec<(DocumentId, f32)> =
             if self.provider.has_native_keyword_search() {
                 self.provider
                     .keyword_search(query, top_k)
@@ -1185,7 +1194,16 @@ impl Rag {
                     })
             } else {
                 self.keyword_search(query, top_k, 0.0)
-            };
+            }
+        };
+        let (vector_search_results, keyword_search_results) =
+            tokio::join!(self.vector_search(query, top_k, 0.0), keyword_leg);
+
+        let vector_search_results = vector_search_results?;
+        debug!("vector_search_results: {vector_search_results:?}",);
+        let vector_search_ids: Vec<DocumentId> =
+            vector_search_results.into_iter().map(|(v, _)| v).collect();
+
         debug!("keyword_search_results: {keyword_search_results:?}",);
         let keyword_search_ids: Vec<DocumentId> =
             keyword_search_results.into_iter().map(|(v, _)| v).collect();
@@ -1842,6 +1860,27 @@ fn select_embedding_model(models: &[&Model]) -> Result<String> {
     Ok(result.value)
 }
 
+pub(crate) fn select_rag_driver() -> Result<String> {
+    let options = vec![
+        "yaml   — portable, in-memory HNSW; usable from several Coyote processes at once (default)",
+        "duckdb — persistent on-disk store; vectors and content survive restarts; HNSW approximate search.",
+    ];
+    let sel = Select::new("RAG storage driver:", options)
+        .with_starting_cursor(0)
+        .prompt()?;
+    if sel.starts_with("duckdb") {
+        println!(
+            "Note: several Coyote processes can query a duckdb RAG at the same time, \
+             but while one process is ingesting or rebuilding it the others cannot \
+             read it until that finishes. Changing its driver later means deleting \
+             and recreating the RAG."
+        );
+        Ok("duckdb".to_string())
+    } else {
+        Ok("yaml".to_string())
+    }
+}
+
 const EXTRACTOR_SKIP: &str = "Skip";
 
 fn select_extractor_model(app: &AppConfig) -> Result<Option<String>> {
@@ -3005,7 +3044,7 @@ mod tests {
 
     #[test]
     fn reciprocal_rank_fusion_empty_lists() {
-        let result = super::reciprocal_rank_fusion(vec![], vec![], 5);
+        let result = reciprocal_rank_fusion(vec![], vec![], 5);
         assert!(result.is_empty(), "empty input should produce empty output");
     }
 
@@ -3013,7 +3052,7 @@ mod tests {
     fn reciprocal_rank_fusion_deduplicates_across_signals() {
         let doc_a = DocumentId::new(0, 0);
         let doc_b = DocumentId::new(0, 1);
-        let result = super::reciprocal_rank_fusion(
+        let result = reciprocal_rank_fusion(
             vec![vec![doc_a, doc_b], vec![doc_a, doc_b]],
             vec![1.0, 1.0],
             5,
@@ -3030,7 +3069,7 @@ mod tests {
     #[test]
     fn reciprocal_rank_fusion_respects_top_k() {
         let docs: Vec<DocumentId> = (0..10).map(|i| DocumentId::new(0, i)).collect();
-        let result = super::reciprocal_rank_fusion(vec![docs], vec![1.0], 3);
+        let result = reciprocal_rank_fusion(vec![docs], vec![1.0], 3);
         assert_eq!(result.len(), 3, "result should be capped at top_k=3");
     }
 
@@ -3038,7 +3077,7 @@ mod tests {
     fn reciprocal_rank_fusion_weights_affect_ranking() {
         let doc_a = DocumentId::new(0, 0);
         let doc_b = DocumentId::new(0, 1);
-        let result = super::reciprocal_rank_fusion(
+        let result = reciprocal_rank_fusion(
             vec![vec![doc_a, doc_b], vec![doc_b, doc_a]],
             vec![10.0, 1.0],
             2,

src/rag/providers/qdrant.rs

@@ -9,6 +9,7 @@ use reqwest::{Client, Response, StatusCode};
 use serde_json::Value;
 use std::collections::HashMap;
 use std::sync::Arc;
+use url::{Host, Url};
 
 /// Marks a `DocumentId` that stands in for a point id Coyote cannot carry
 /// directly. Qdrant accepts UUID strings as point ids, and that is what
@@ -104,7 +105,7 @@ fn parse_search_hits(
             let score = pt["score"].as_f64()? as f32;
             Some((interner.document_id(&pt["id"])?, score))
         })
-        .filter(|(_, score)| *score > min_score)
+        .filter(|(_, score)| min_score <= 0.0 || *score > min_score)
         .collect())
 }
 
@@ -183,7 +184,22 @@ pub struct QdrantProvider {
 }
 
 impl QdrantProvider {
-    fn make_client(api_key: Option<&str>) -> Result<Client> {
+    fn skips_proxy(base_url: &str) -> bool {
+        let Ok(url) = Url::parse(base_url) else {
+            return false;
+        };
+        match url.host() {
+            Some(Host::Domain(name)) => {
+                name == "localhost" || name.ends_with(".localhost") || name.ends_with(".local")
+            }
+            Some(Host::Ipv4(ip)) => ip.is_loopback() || ip.is_private() || ip.is_link_local(),
+            // No stable is_unique_local, so fc00::/7 is matched directly.
+            Some(Host::Ipv6(ip)) => ip.is_loopback() || ip.segments()[0] & 0xfe00 == 0xfc00,
+            None => false,
+        }
+    }
+
+    fn make_client(base_url: &str, api_key: Option<&str>) -> Result<Client> {
         let mut headers = HeaderMap::new();
         if let Some(key) = api_key {
             let mut value =
@@ -191,10 +207,11 @@ impl QdrantProvider {
             value.set_sensitive(true);
             headers.insert("api-key", value);
         }
-        Client::builder()
+        let mut builder = Client::builder().default_headers(headers);
-            .default_headers(headers)
+        if Self::skips_proxy(base_url) {
-            .build()
+            builder = builder.no_proxy();
-            .context("Failed to build reqwest client")
+        }
+        builder.build().context("Failed to build reqwest client")
     }
 
     pub(crate) fn normalize_base_url(host: &str) -> String {
@@ -219,7 +236,7 @@ impl QdrantProvider {
         api_key: Option<&str>,
     ) -> Result<Value> {
         let base_url = Self::normalize_base_url(host);
-        let client = Self::make_client(api_key)?;
+        let client = Self::make_client(&base_url, api_key)?;
         let resp = client
             .get(format!("{base_url}/collections/{collection}"))
             .send()
@@ -237,7 +254,7 @@ impl QdrantProvider {
 
     pub async fn new(host: &str, collection: &str, api_key: Option<&str>) -> Result<Self> {
         let base_url = Self::normalize_base_url(host);
-        let client = Self::make_client(api_key)?;
+        let client = Self::make_client(&base_url, api_key)?;
         let resp = client
             .get(format!("{base_url}/collections/{collection}"))
             .send()
@@ -260,7 +277,7 @@ impl QdrantProvider {
 
     pub async fn list_collections(host: &str, api_key: Option<&str>) -> Result<Vec<String>> {
         let base_url = Self::normalize_base_url(host);
-        let client = Self::make_client(api_key)?;
+        let client = Self::make_client(&base_url, api_key)?;
         let resp = client
             .get(format!("{base_url}/collections"))
             .send()
@@ -310,7 +327,7 @@ impl QdrantProvider {
         api_key: Option<&str>,
     ) -> Result<Option<String>> {
         let base_url = Self::normalize_base_url(host);
-        let client = Self::make_client(api_key)?;
+        let client = Self::make_client(&base_url, api_key)?;
         let url = format!("{base_url}/collections/{collection}/points/scroll");
         let body = serde_json::json!({ "limit": 1, "with_payload": false });
 
@@ -353,7 +370,8 @@ impl RagProvider for QdrantProvider {
         // `score_threshold` is deliberately NOT sent. It is metric-aware: on Cosine
         // collections 0.0 means "no floor" as expected, but Euclid collections score
         // by negative distance, where 0.0 filters everything out. The attach wizard
-        // does not pin the distance metric, so filter locally instead.
+        // does not pin the distance metric, so filter locally instead; i.e. where a
+        // 0.0 floor is correctly treated as "no floor" (see `parse_search_hits`).
         let body = serde_json::json!({
             "vector": embedding,
             "limit": top_k,
@@ -576,6 +594,73 @@ mod tests {
         assert!(provider.fetch_content(&[]).await.unwrap().is_empty());
     }
 
+    #[test]
+    fn local_and_private_hosts_skip_the_proxy() {
+        for host in [
+            "http://localhost:6333",
+            "http://127.0.0.1:6333",
+            "http://192.168.0.56:6333",
+            "http://10.1.2.3:6333",
+            "http://172.16.4.5:6333",
+            "http://qdrant.local:6333",
+            "http://[::1]:6333",
+        ] {
+            assert!(
+                QdrantProvider::skips_proxy(host),
+                "{host} should not be proxied"
+            );
+        }
+    }
+
+    #[test]
+    fn public_hosts_still_honour_the_environment() {
+        for host in [
+            "https://qdrant.example.com",
+            "http://8.8.8.8:6333",
+            "https://xyz.eu-central.aws.cloud.qdrant.io:6333",
+            "http://172.32.0.1:6333",
+        ] {
+            assert!(
+                !QdrantProvider::skips_proxy(host),
+                "{host} must keep the environment's proxy"
+            );
+        }
+    }
+
+    /// Euclid collections score by NEGATIVE distance, so the 0.0 the caller
+    /// passes must mean "no floor". Filtering on it drops every hit — the exact
+    /// bug that keeps Qdrant's own `score_threshold` off the wire.
+    #[test]
+    fn a_zero_floor_keeps_negative_euclid_scores() {
+        let mut interner = PointIdInterner::default();
+        let search = serde_json::json!({
+            "result": [
+                {"id": 1, "score": -0.12},
+                {"id": 2, "score": -8.5},
+            ]
+        });
+
+        let hits = parse_search_hits(&mut interner, &search, 0.0).unwrap();
+
+        assert_eq!(hits.len(), 2, "a 0.0 floor must not drop negative scores");
+    }
+
+    #[test]
+    fn a_positive_floor_still_filters() {
+        let mut interner = PointIdInterner::default();
+        let search = serde_json::json!({
+            "result": [
+                {"id": 1, "score": 0.9},
+                {"id": 2, "score": 0.2},
+            ]
+        });
+
+        let hits = parse_search_hits(&mut interner, &search, 0.5).unwrap();
+
+        assert_eq!(hits.len(), 1);
+        assert_eq!(hits[0].0, DocumentId(1));
+    }
+
     /// A UUID-keyed collection has to survive the whole `vector_search` →
     /// `fetch_content` round trip, and the fetch must ask Qdrant for the ORIGINAL
     /// string id. Parsing ids with `as_u64()` used to drop these hits inside a

src/render/markdown.rs

@@ -39,8 +39,10 @@ static INLINE_CODE_RE: LazyLock<Regex> = LazyLock::new(|| Regex::new(r"`([^`\n]+
 static IMAGE_RE: LazyLock<Regex> =
     LazyLock::new(|| Regex::new(r"!\[([^\]]*)\]\(([^)]+)\)").unwrap());
 static LINK_RE: LazyLock<Regex> = LazyLock::new(|| Regex::new(r"\[([^\]]+)\]\(([^)]+)\)").unwrap());
-static BOLD_AST_RE: LazyLock<Regex> = LazyLock::new(|| Regex::new(r"\*\*([^*\n]+)\*\*").unwrap());
+static BOLD_AST_RE: LazyLock<Regex> =
-static BOLD_US_RE: LazyLock<Regex> = LazyLock::new(|| Regex::new(r"__([^_\n]+)__").unwrap());
+    LazyLock::new(|| Regex::new(r"\*\*((?:[^*\n]|\*(?!\*))+?)\*\*").unwrap());
+static BOLD_US_RE: LazyLock<Regex> =
+    LazyLock::new(|| Regex::new(r"__((?:[^_\n]|_(?!_))+?)__").unwrap());
 static ITALIC_AST_RE: LazyLock<Regex> =
     LazyLock::new(|| Regex::new(r"(?<![*\w])\*(?!\s)([^*\n]+?)(?<!\s)\*(?!\*)").unwrap());
 static ITALIC_US_RE: LazyLock<Regex> =
@@ -2419,6 +2421,36 @@ std::error::Error>> {
         assert!(result.contains("\x1b[9m"), "strikethrough SGR: {result:?}");
     }
 
+    #[test]
+    fn bold_asterisk_wraps_italic_asterisk() {
+        let styles = test_styles();
+
+        let result = apply_inline("**loud *soft* loud**", &styles);
+
+        assert!(
+            !result.contains("**"),
+            "outer bold markers stripped: {result:?}"
+        );
+        assert!(result.contains("\x1b[1m"), "bold SGR present: {result:?}");
+        assert!(result.contains("\x1b[3m"), "italic SGR present: {result:?}");
+        assert!(result.contains("soft"));
+    }
+
+    #[test]
+    fn bold_underscore_wraps_italic_underscore() {
+        let styles = test_styles();
+
+        let result = apply_inline("__loud _soft_ loud__", &styles);
+
+        assert!(
+            !result.contains("__"),
+            "outer bold markers stripped: {result:?}"
+        );
+        assert!(result.contains("\x1b[1m"), "bold SGR present: {result:?}");
+        assert!(result.contains("\x1b[3m"), "italic SGR present: {result:?}");
+        assert!(result.contains("soft"));
+    }
+
     #[test]
     fn bold_wraps_inline_code() {
         let styles = test_styles();

src/repl/mod.rs

@@ -892,7 +892,7 @@ pub async fn run_repl_command(
             ".rag" => match split_first_arg(args) {
                 Some(("attach", rest)) => match rest {
                     Some(name) if !name.trim().is_empty() => {
-                        ctx.attach_rag(name.trim()).await?;
+                        ctx.attach_rag(name.trim(), abort_signal.clone()).await?;
                     }
                     _ => println!("Usage: .rag attach <name>"),
                 },

src/sandbox/mixins.rs

@@ -1,9 +1,10 @@
 use std::env;
 use std::fs;
 use std::fs::{read_dir, read_to_string};
+use std::io;
 use std::path::{Path, PathBuf};
 
-use anyhow::{Context, Result};
+use anyhow::{Context, Result, anyhow, bail};
 use serde_yaml::Value;
 use sha2::{Digest, Sha256};
 
@@ -12,6 +13,7 @@ use crate::config::paths;
 const SBX_MIXIN_FILE_NAME: &str = "sbx-mixin.yaml";
 const SBX_MIXIN_FILE_SUFFIX: &str = ".sbx-mixin.yaml";
 const KIT_SPEC_FILE_NAME: &str = "spec.yaml";
+const MIXIN_FILES_DIR_NAME: &str = "files";
 
 #[derive(Debug, Clone)]
 pub struct DiscoveredMixin {
@@ -34,33 +36,152 @@ impl DiscoveredMixin {
 pub fn wrap_mixin_as_kit(mixin_path: &Path) -> Result<PathBuf> {
     let bytes = fs::read(mixin_path)
         .with_context(|| format!("Failed to read sbx mixin {}", mixin_path.display()))?;
-    wrap_mixin_bytes_as_kit(&bytes, &mixin_path.display().to_string())
+    let label = mixin_path.display().to_string();
+
+    let files = mixin_path
+        .parent()
+        .map(|p| p.join(MIXIN_FILES_DIR_NAME))
+        .filter(|p| p.is_dir())
+        .map(|dir| collect_staged_files(&dir))
+        .transpose()?
+        .unwrap_or_default();
+
+    stage_kit(&bytes, &files, &label)
 }
 
 pub fn wrap_mixin_bytes_as_kit(bytes: &[u8], label: &str) -> Result<PathBuf> {
+    stage_kit(bytes, &[], label)
+}
+
+struct StagedFile {
+    relpath: PathBuf,
+    mode: u32,
+    bytes: Vec<u8>,
+}
+
+fn stage_kit(spec_bytes: &[u8], files: &[StagedFile], label: &str) -> Result<PathBuf> {
     let mut hasher = Sha256::new();
-    hasher.update(bytes);
+    hasher.update(spec_bytes);
+    for f in files {
+        let rel_str = f.relpath.to_str().ok_or_else(|| {
+            anyhow!(
+                "Non-UTF-8 path inside mixin {MIXIN_FILES_DIR_NAME}/: {}",
+                f.relpath.display()
+            )
+        })?;
+        hasher.update(b"\0COYOTE_MIXIN_FILE\0");
+        hasher.update((rel_str.len() as u64).to_le_bytes());
+        hasher.update(rel_str.as_bytes());
+        hasher.update(f.mode.to_le_bytes());
+        hasher.update((f.bytes.len() as u64).to_le_bytes());
+        hasher.update(&f.bytes);
+    }
     let hash = format!("{:x}", hasher.finalize());
 
     let kit_dir = paths::sbx_mixin_kits_dir().join(&hash);
     let spec_path = kit_dir.join(KIT_SPEC_FILE_NAME);
+    let files_dst = kit_dir.join(MIXIN_FILES_DIR_NAME);
 
-    if let Ok(existing) = fs::read(&spec_path)
+    let spec_matches = fs::read(&spec_path).is_ok_and(|existing| existing == spec_bytes);
-        && existing == bytes
+    let files_ready = files.is_empty() || files_dst.is_dir();
-    {
+    if spec_matches && files_ready {
         return Ok(kit_dir);
     }
 
     fs::create_dir_all(&kit_dir)
         .with_context(|| format!("Failed to create mixin kit dir {}", kit_dir.display()))?;
-    fs::write(&spec_path, bytes)
+    fs::write(&spec_path, spec_bytes)
         .with_context(|| format!("Failed to write {}", spec_path.display()))?;
 
+    if !files.is_empty() {
+        if files_dst.exists() {
+            fs::remove_dir_all(&files_dst).with_context(|| {
+                format!(
+                    "Failed to clear stale mixin files at {}",
+                    files_dst.display()
+                )
+            })?;
+        }
+        for f in files {
+            let dst = files_dst.join(&f.relpath);
+            if let Some(parent) = dst.parent() {
+                fs::create_dir_all(parent)
+                    .with_context(|| format!("Failed to create dir {}", parent.display()))?;
+            }
+            fs::write(&dst, &f.bytes)
+                .with_context(|| format!("Failed to write staged mixin file {}", dst.display()))?;
+            #[cfg(unix)]
+            {
+                use std::os::unix::fs::PermissionsExt;
+                fs::set_permissions(&dst, fs::Permissions::from_mode(f.mode))
+                    .with_context(|| format!("Failed to set mode on {}", dst.display()))?;
+            }
+        }
+    }
+
     debug!("Wrapped mixin {label} as kit at {}", kit_dir.display());
 
     Ok(kit_dir)
 }
 
+fn collect_staged_files(root: &Path) -> Result<Vec<StagedFile>> {
+    let mut out = Vec::new();
+    walk_staged_files(root, Path::new(""), &mut out)?;
+    Ok(out)
+}
+
+fn walk_staged_files(abs_dir: &Path, rel_dir: &Path, out: &mut Vec<StagedFile>) -> Result<()> {
+    let rd = fs::read_dir(abs_dir)
+        .with_context(|| format!("Failed to read mixin files dir {}", abs_dir.display()))?;
+    let mut entries: Vec<_> = rd
+        .collect::<io::Result<Vec<_>>>()
+        .with_context(|| format!("Failed to iterate mixin files dir {}", abs_dir.display()))?;
+    entries.sort_by_key(|e| e.file_name());
+
+    for entry in entries {
+        let file_type = entry
+            .file_type()
+            .with_context(|| format!("Failed to stat {}", entry.path().display()))?;
+        let abs = entry.path();
+        let rel = rel_dir.join(entry.file_name());
+
+        if file_type.is_symlink() {
+            bail!(
+                "Symlinks are not allowed inside a mixin {MIXIN_FILES_DIR_NAME}/ tree: {}",
+                abs.display()
+            );
+        }
+
+        if file_type.is_dir() {
+            walk_staged_files(&abs, &rel, out)?;
+        } else if file_type.is_file() {
+            let bytes = fs::read(&abs)
+                .with_context(|| format!("Failed to read staged mixin file {}", abs.display()))?;
+            let mode = staged_file_mode(&entry)?;
+            out.push(StagedFile {
+                relpath: rel,
+                mode,
+                bytes,
+            });
+        }
+    }
+    Ok(())
+}
+
+#[cfg(unix)]
+fn staged_file_mode(entry: &fs::DirEntry) -> Result<u32> {
+    use std::os::unix::fs::PermissionsExt;
+    let meta = entry
+        .metadata()
+        .with_context(|| format!("Failed to stat {}", entry.path().display()))?;
+    Ok(meta.permissions().mode() & 0o777)
+}
+
+#[cfg(not(unix))]
+fn staged_file_mode(_entry: &fs::DirEntry) -> Result<u32> {
+    Ok(0o644)
+}
+
 pub fn discover() -> Result<Vec<DiscoveredMixin>> {
     let mut out = Vec::new();
 
@@ -556,6 +677,196 @@ network:
                 "kit_path should not return the original file path"
             );
         }
+
+        fn write_staged_file(mixin: &Path, rel: &str, content: &[u8]) {
+            let dst = mixin.parent().unwrap().join(MIXIN_FILES_DIR_NAME).join(rel);
+            fs::create_dir_all(dst.parent().unwrap()).unwrap();
+            fs::write(&dst, content).unwrap();
+        }
+
+        #[test]
+        #[serial]
+        fn wrap_mixin_as_kit_copies_sibling_files_tree_into_kit() {
+            let _guard = TestCacheDirGuard::new();
+            let mixin = write_mixin("files-copy", "kind: mixin\nname: probe\n");
+            write_staged_file(&mixin, "home/hello.md", b"# hello\n");
+            write_staged_file(&mixin, "home/nested/deep.txt", b"deep\n");
+
+            let kit_dir = wrap_mixin_as_kit(&mixin).unwrap();
+
+            assert!(kit_dir.join("spec.yaml").exists());
+            let files_root = kit_dir.join(MIXIN_FILES_DIR_NAME);
+            assert!(files_root.is_dir(), "kit dir must contain a files/ tree");
+            assert_eq!(
+                fs::read(files_root.join("home/hello.md")).unwrap(),
+                b"# hello\n"
+            );
+            assert_eq!(
+                fs::read(files_root.join("home/nested/deep.txt")).unwrap(),
+                b"deep\n"
+            );
+        }
+
+        #[test]
+        #[serial]
+        fn wrap_mixin_as_kit_hash_changes_when_a_staged_file_is_edited() {
+            let _guard = TestCacheDirGuard::new();
+            let mixin = write_mixin("files-hash-content", "kind: mixin\nname: probe\n");
+            write_staged_file(&mixin, "home/note.md", b"before\n");
+            let kit_before = wrap_mixin_as_kit(&mixin).unwrap();
+
+            write_staged_file(&mixin, "home/note.md", b"after\n");
+            let kit_after = wrap_mixin_as_kit(&mixin).unwrap();
+
+            assert_ne!(
+                kit_before, kit_after,
+                "editing a staged file must invalidate the kit hash"
+            );
+            assert_eq!(
+                fs::read(kit_after.join("files/home/note.md")).unwrap(),
+                b"after\n"
+            );
+        }
+
+        #[test]
+        #[serial]
+        fn wrap_mixin_as_kit_hash_changes_when_a_staged_file_is_added() {
+            let _guard = TestCacheDirGuard::new();
+            let mixin = write_mixin("files-hash-added", "kind: mixin\nname: probe\n");
+            write_staged_file(&mixin, "home/one.md", b"one\n");
+            let kit_before = wrap_mixin_as_kit(&mixin).unwrap();
+
+            write_staged_file(&mixin, "home/two.md", b"two\n");
+            let kit_after = wrap_mixin_as_kit(&mixin).unwrap();
+
+            assert_ne!(
+                kit_before, kit_after,
+                "adding a staged file must invalidate the kit hash"
+            );
+        }
+
+        #[test]
+        #[serial]
+        fn wrap_mixin_as_kit_hash_unchanged_when_no_files_dir() {
+            let _guard = TestCacheDirGuard::new();
+            let content = "kind: mixin\nname: legacy\n";
+            let mixin = write_mixin("legacy-no-files", content);
+
+            let with_helper = wrap_mixin_as_kit(&mixin).unwrap();
+            let bytes_only = wrap_mixin_bytes_as_kit(content.as_bytes(), "legacy").unwrap();
+
+            assert_eq!(
+                with_helper, bytes_only,
+                "mixins without a sibling files/ must keep the legacy bytes-only hash to reuse existing cache dirs"
+            );
+        }
+
+        #[test]
+        #[serial]
+        fn wrap_mixin_as_kit_ignores_sibling_files_that_is_not_a_directory() {
+            let _guard = TestCacheDirGuard::new();
+            let content = "kind: mixin\nname: probe\n";
+            let mixin = write_mixin("files-not-a-dir", content);
+            fs::write(mixin.parent().unwrap().join(MIXIN_FILES_DIR_NAME), b"decoy").unwrap();
+
+            let wrapped = wrap_mixin_as_kit(&mixin).unwrap();
+            let bytes_only = wrap_mixin_bytes_as_kit(content.as_bytes(), "probe").unwrap();
+
+            assert_eq!(
+                wrapped, bytes_only,
+                "a regular file named files must be ignored, not staged"
+            );
+            assert!(!wrapped.join(MIXIN_FILES_DIR_NAME).exists());
+        }
+
+        #[test]
+        #[serial]
+        fn wrap_mixin_as_kit_rebuilds_files_when_cache_dir_missing_files_tree() {
+            let _guard = TestCacheDirGuard::new();
+            let mixin = write_mixin("files-rebuild", "kind: mixin\nname: probe\n");
+            write_staged_file(&mixin, "home/hello.md", b"hi\n");
+
+            let kit_dir = wrap_mixin_as_kit(&mixin).unwrap();
+            let files_dst = kit_dir.join(MIXIN_FILES_DIR_NAME);
+            fs::remove_dir_all(&files_dst).unwrap();
+            assert!(!files_dst.exists());
+
+            let kit_again = wrap_mixin_as_kit(&mixin).unwrap();
+
+            assert_eq!(kit_again, kit_dir, "kit path is content-addressed");
+            assert!(
+                files_dst.is_dir(),
+                "a partial cache (spec present, files/ missing) must be rebuilt"
+            );
+            assert_eq!(fs::read(files_dst.join("home/hello.md")).unwrap(), b"hi\n");
+        }
+
+        #[test]
+        #[serial]
+        fn wrap_mixin_as_kit_deterministic_with_staged_files() {
+            let _guard = TestCacheDirGuard::new();
+            let content = "kind: mixin\nname: probe\n";
+            let mixin_one = write_mixin("determ-1", content);
+            write_staged_file(&mixin_one, "home/note.md", b"same\n");
+            let mixin_two = write_mixin("determ-2", content);
+            write_staged_file(&mixin_two, "home/note.md", b"same\n");
+
+            let kit_a = wrap_mixin_as_kit(&mixin_one).unwrap();
+            let kit_b = wrap_mixin_as_kit(&mixin_two).unwrap();
+
+            assert_eq!(
+                kit_a, kit_b,
+                "identical spec+files must produce the same content-addressed kit dir"
+            );
+        }
+
+        #[cfg(unix)]
+        #[test]
+        #[serial]
+        fn wrap_mixin_as_kit_rejects_symlinks_inside_files_tree() {
+            use std::os::unix::fs::symlink;
+
+            let _guard = TestCacheDirGuard::new();
+            let mixin = write_mixin("files-symlink", "kind: mixin\nname: probe\n");
+            let files_dir = mixin.parent().unwrap().join(MIXIN_FILES_DIR_NAME);
+            fs::create_dir_all(&files_dir).unwrap();
+            let target = files_dir.join("target.txt");
+            fs::write(&target, b"real").unwrap();
+            symlink(&target, files_dir.join("link.txt")).unwrap();
+
+            let err = wrap_mixin_as_kit(&mixin).unwrap_err();
+            let msg = format!("{err:#}");
+            assert!(
+                msg.contains("Symlinks are not allowed"),
+                "expected symlink rejection, got: {msg}"
+            );
+        }
+
+        #[cfg(unix)]
+        #[test]
+        #[serial]
+        fn wrap_mixin_as_kit_preserves_executable_bit() {
+            use std::os::unix::fs::PermissionsExt;
+
+            let _guard = TestCacheDirGuard::new();
+            let mixin = write_mixin("files-exec", "kind: mixin\nname: probe\n");
+            write_staged_file(&mixin, "bin/run.sh", b"#!/bin/sh\necho hi\n");
+            let src = mixin
+                .parent()
+                .unwrap()
+                .join(MIXIN_FILES_DIR_NAME)
+                .join("bin/run.sh");
+            fs::set_permissions(&src, fs::Permissions::from_mode(0o755)).unwrap();
+
+            let kit_dir = wrap_mixin_as_kit(&mixin).unwrap();
+            let dst = kit_dir.join("files/bin/run.sh");
+            let mode = fs::metadata(&dst).unwrap().permissions().mode() & 0o777;
+
+            assert_eq!(
+                mode, 0o755,
+                "executable bit must survive the copy into the kit dir"
+            );
+        }
     }
 
     #[test]

src/sandbox/mod.rs

@@ -337,29 +337,20 @@ fn inject_rag_secrets(vault: &Vault, registered: &HashSet<String>) -> Result<()>
         if !data.attached {
             continue;
         }
-        let Some(placeholder) = data.driver_config.get("api_key") else {
+        let secret_names = driver_config_secret_names(&data);
+        let Some((primary, extra)) = secret_names.split_first() else {
             continue;
         };
-        let service_id = mcp_credentials::secret_service_id(&stem);
-        if service_id.is_empty() || registered.contains(&service_id) {
-            continue;
-        }
-        let secret_name = placeholder
-            .trim_start_matches("{{")
-            .trim_end_matches("}}")
-            .trim();
 
-        match vault.get_secret(secret_name, false) {
+        let service_id = mcp_credentials::secret_service_id(&stem);
-            Ok(secret_value) => {
+        if !service_id.is_empty() && !registered.contains(&service_id) {
-                sbx_secret_set(&service_id, &secret_value)
+            bind_rag_secret(vault, &service_id, primary, &stem)?;
-                    .context("Failed to register RAG secret with sbx")?;
+        }
-            }
+
-            Err(e) => {
+        for name in extra {
-                eprintln!(
+            let id = mcp_credentials::secret_service_id(name);
-                    "Warning: could not load secret '{secret_name}' for RAG '{stem}': {e}. \
+            if !id.is_empty() && !registered.contains(&id) {
-                     Queries to this RAG will fail inside the sandbox. \
+                bind_rag_secret(vault, &id, name, &stem)?;
-                     Run `coyote --add-secret {secret_name}` to fix."
-                );
             }
         }
     }
@@ -367,6 +358,43 @@ fn inject_rag_secrets(vault: &Vault, registered: &HashSet<String>) -> Result<()>
     Ok(())
 }
 
+fn driver_config_secret_names(data: &RagData) -> Vec<String> {
+    let mut names: Vec<String> = Vec::new();
+    for value in data.driver_config.values() {
+        let trimmed = value.trim();
+        let Ok(Some(caps)) = SECRET_RE.captures(trimmed) else {
+            continue;
+        };
+        if caps.get(0).map(|m| m.as_str()) != Some(trimmed) {
+            continue;
+        }
+        let Some(name) = caps.get(1).map(|m| m.as_str().trim()) else {
+            continue;
+        };
+        if !name.is_empty() && !names.iter().any(|n| n == name) {
+            names.push(name.to_string());
+        }
+    }
+    names
+}
+
+fn bind_rag_secret(vault: &Vault, service_id: &str, secret_name: &str, stem: &str) -> Result<()> {
+    match vault.get_secret(secret_name, false) {
+        Ok(secret_value) => {
+            sbx_secret_set(service_id, &secret_value)
+                .context("Failed to register RAG secret with sbx")?;
+        }
+        Err(e) => {
+            eprintln!(
+                "Warning: could not load secret '{secret_name}' for RAG '{stem}': {e}. \
+                 Queries to this RAG will fail inside the sandbox. \
+                 Run `coyote --add-secret {secret_name}` to fix."
+            );
+        }
+    }
+    Ok(())
+}
+
 fn provider_to_sbx_service(provider_type: &str, client_name: Option<&str>) -> String {
     match provider_type {
         "claude" => "anthropic".to_string(),
@@ -646,6 +674,64 @@ fn chown_agent_recursive(sandbox: &str, path: &str) -> Result<()> {
 #[cfg(test)]
 mod tests {
     use super::*;
+
+    fn rag_with(driver_config: &[(&str, &str)]) -> RagData {
+        let mut data = RagData::new("m".into(), 1024, 50, None, 5, None, Default::default());
+        data.driver = "qdrant".to_string();
+        data.attached = true;
+        for (k, v) in driver_config {
+            data.driver_config.insert(k.to_string(), v.to_string());
+        }
+        data
+    }
+
+    #[test]
+    fn secret_names_are_found_whatever_the_field_is_called() {
+        let data = rag_with(&[
+            ("host", "qdrant.example.com:6333"),
+            ("collection", "docs"),
+            ("token", "{{SOME_TOKEN}}"),
+        ]);
+
+        assert_eq!(driver_config_secret_names(&data), vec!["SOME_TOKEN"]);
+    }
+
+    #[test]
+    fn a_literal_credential_is_not_treated_as_a_secret_name() {
+        let data = rag_with(&[("api_key", "sk-a-real-looking-key")]);
+
+        assert!(driver_config_secret_names(&data).is_empty());
+    }
+
+    #[test]
+    fn plain_values_are_never_mistaken_for_secrets() {
+        let data = rag_with(&[("host", "localhost:6333"), ("collection", "docs")]);
+
+        assert!(driver_config_secret_names(&data).is_empty());
+    }
+
+    #[test]
+    fn a_partial_placeholder_is_not_a_credential() {
+        let data = rag_with(&[("api_key", "Bearer {{KEY}}")]);
+
+        assert!(driver_config_secret_names(&data).is_empty());
+    }
+
+    #[test]
+    fn several_secrets_are_all_found_and_deduped() {
+        let data = rag_with(&[
+            ("api_key", "{{QDRANT_KEY}}"),
+            ("host", "localhost:6333"),
+            ("token", "{{ OTHER_TOKEN }}"),
+            ("fallback_key", "{{QDRANT_KEY}}"),
+        ]);
+
+        assert_eq!(
+            driver_config_secret_names(&data),
+            vec!["QDRANT_KEY", "OTHER_TOKEN"],
+            "order follows driver_config, and a repeat is not registered twice"
+        );
+    }
     use std::time::{SystemTime, UNIX_EPOCH};
 
     #[test]