fix: address code review findings on the bundle lifecycle

The user-origin marker on replaced mcp.json entries is now sticky:
re-records and cross-bundle transfers only upgrade replaced to
transferred when the prior record proves bundle origin, so updating a
bundle can no longer make uninstall delete a key the user had before the
bundle replaced it. Canonical source URLs lowercase only the host, since
self-hosted forges treat repository paths as case-sensitive and
collapsing distinct repos misdirects updates and uninstalls. git clone
invocations pass '--' before the URL so a crafted source cannot be
parsed as a git flag. Lifecycle flags (--install, --install-builtins,
--update-bundle, --uninstall) and their companions now conflict
explicitly instead of first-match dispatch silently dropping actions.
--install-from returns as a hidden tombstone that errors with the
replacement instead of feeding the flag to the LLM as prompt text.
--list-bundles dispatches before config load so a pure read no longer
boots MCP servers. write_file_atomic fsyncs before the rename so a crash
cannot persist a truncated store. REPL: .uninstall accepts --yes,
.install rejects trailing tokens after a category, and .install remote
gets a migration hint. Plus polish: host validation rejects '#' and '?',
renamed_to no longer serializes null, derived names get a debug assert
against the validator, completions share DEFAULT_GIT_HOST, README
mentions skills.

src/cli/mod.rs

@@ -180,27 +180,37 @@ pub struct Cli {
     #[arg(long, help_heading = "List & Discovery")]
     pub list_bundles: bool,
 
-    /// Install assets from a remote git repository (URL may be suffixed with #<ref>), or update an already-installed bundle by name
+    /// Install assets from a remote git repository (a URL or <owner>/<repo> shorthand, optionally suffixed with #<ref>), or update an already-installed bundle by name
     #[arg(
         long,
-        value_name = "GIT_URL|NAME",
+        value_name = "GIT_URL|OWNER/REPO|NAME",
+        conflicts_with_all = ["install_builtins", "update_bundle", "uninstall"],
         help_heading = "Installation & Updates"
     )]
     pub install: Option<String>,
-    /// Git host used to expand <owner>/<repo> shorthand values passed to --install
+    /// Git host used to expand <owner>/<repo> shorthand values passed to --install (also forces the value to be treated as a source when it matches an installed bundle name)
     #[arg(
         long,
         value_name = "HOST",
         requires = "install",
+        conflicts_with_all = ["install_builtins", "update_bundle", "uninstall"],
         help_heading = "Installation & Updates"
     )]
     pub git_host: Option<String>,
-    /// Reinstall bundled assets, overwriting any local changes
+    /// Removed; use --install <GIT_URL> instead
+    #[arg(
+        long,
+        hide = true,
+        value_name = "GIT_URL",
+        help_heading = "Installation & Updates"
+    )]
+    pub install_from: Option<String>,
+    /// Reinstall bundled assets for a category (asks before overwriting your local changes)
     #[arg(
         long,
         value_name = "CATEGORY",
         value_enum,
-        conflicts_with_all = ["install"],
+        conflicts_with_all = ["update_bundle", "uninstall"],
         help_heading = "Installation & Updates"
     )]
     pub install_builtins: Option<AssetCategory>,
@@ -210,20 +220,36 @@ pub struct Cli {
         value_name = "CATEGORY",
         value_enum,
         requires = "install",
+        conflicts_with_all = ["install_builtins", "update_bundle", "uninstall"],
         help_heading = "Installation & Updates"
     )]
     pub filter: Option<InstallFilter>,
     /// Overwrite all conflicts without prompting (used with --install)
-    #[arg(long, requires = "install", help_heading = "Installation & Updates")]
+    #[arg(
+        long,
+        requires = "install",
+        conflicts_with_all = ["install_builtins", "update_bundle", "uninstall"],
+        help_heading = "Installation & Updates"
+    )]
     pub install_force: bool,
     /// Update an installed bundle from its recorded source (NAME may be suffixed with #<ref> to move a pin)
-    #[arg(long, value_name = "NAME", help_heading = "Installation & Updates")]
+    #[arg(
+        long,
+        value_name = "NAME",
+        conflicts_with_all = ["uninstall"],
+        help_heading = "Installation & Updates"
+    )]
     pub update_bundle: Option<String>,
     /// Uninstall a bundle: delete its owned files and remove its mcp.json entries
     #[arg(long, value_name = "NAME", help_heading = "Installation & Updates")]
     pub uninstall: Option<String>,
     /// Skip uninstall confirmation prompts (locally modified items are still kept)
-    #[arg(long, requires = "uninstall", help_heading = "Installation & Updates")]
+    #[arg(
+        long,
+        requires = "uninstall",
+        conflicts_with_all = ["install", "install_builtins", "update_bundle"],
+        help_heading = "Installation & Updates"
+    )]
     pub yes: bool,
     /// Sync models updates
     #[arg(long, help_heading = "Installation & Updates")]
@@ -572,10 +598,11 @@ mod tests {
     }
 
     #[test]
-    fn parse_install_from_is_no_longer_a_flag() {
+    fn parse_install_from_is_a_tombstone() {
         let cli = parse(&["--install-from", "https://github.com/x/y"]);
         assert!(cli.install.is_none());
-        assert_eq!(cli.text, vec!["--install-from", "https://github.com/x/y"]);
+        assert_eq!(cli.install_from.as_deref(), Some("https://github.com/x/y"));
+        assert!(cli.text.is_empty());
     }
 
     #[test]
@@ -586,6 +613,28 @@ mod tests {
         );
     }
 
+    #[test]
+    fn parse_lifecycle_flags_are_mutually_exclusive() {
+        assert!(Cli::try_parse_from(["coyote", "--install", "x", "--uninstall", "y"]).is_err());
+        assert!(
+            Cli::try_parse_from(["coyote", "--update-bundle", "x", "--uninstall", "y"]).is_err()
+        );
+        assert!(
+            Cli::try_parse_from(["coyote", "--install-builtins", "agents", "--uninstall", "y"])
+                .is_err()
+        );
+        assert!(Cli::try_parse_from(["coyote", "--install", "x", "--update-bundle", "y"]).is_err());
+    }
+
+    #[test]
+    fn parse_companion_flags_conflict_with_other_lifecycle_actions() {
+        assert!(
+            Cli::try_parse_from(["coyote", "--update-bundle", "x", "--filter", "agents"]).is_err()
+        );
+        assert!(Cli::try_parse_from(["coyote", "--uninstall", "x", "--install-force"]).is_err());
+        assert!(Cli::try_parse_from(["coyote", "--install", "x", "--yes"]).is_err());
+    }
+
     #[test]
     fn parse_filter_requires_install() {
         assert!(Cli::try_parse_from(["coyote", "--filter", "agents"]).is_err());
@@ -604,6 +653,10 @@ mod tests {
     #[test]
     fn parse_git_host_requires_install() {
         assert!(Cli::try_parse_from(["coyote", "--git-host", "git.x.com"]).is_err());
+        assert!(
+            Cli::try_parse_from(["coyote", "--git-host", "gitlab.com", "--update-bundle", "x"])
+                .is_err()
+        );
         assert_eq!(
             parse(&["--install", "someuser/omc", "--git-host", "git.x.com"])
                 .git_host

src/config/bundles.rs

@@ -45,6 +45,7 @@ pub(crate) struct FileRecord {
 pub(crate) struct McpServerRecord {
     pub(crate) name: String,
     pub(crate) action: McpAction,
+    #[serde(default, skip_serializing_if = "Option::is_none")]
     pub(crate) renamed_to: Option<String>,
     /// Hash of the mcp.json entry as written; a later mismatch means the user
     /// modified it. Absent on records made before entry hashing existed.
@@ -299,6 +300,10 @@ impl BundleStore {
             );
         }
 
+        debug_assert!(
+            validate_bundle_name(&resolved.name).is_ok(),
+            "derived bundle names must satisfy validate_bundle_name"
+        );
         Ok(resolved)
     }
 
@@ -391,8 +396,10 @@ impl BundleStore {
     }
 
     /// An entry whose key any bundle already owns transfers to `bundle`, and
-    /// its `replaced` action upgrades to `transferred`; plain `replaced`
-    /// marks a pre-existing user entry that uninstall must never delete.
+    /// its `replaced` action upgrades to `transferred` only when the prior
+    /// record proves bundle origin. A prior `replaced` record marks a
+    /// pre-existing user entry that uninstall must never delete, and that
+    /// marker survives re-records and cross-bundle transfers.
     pub(crate) fn record_mcp_servers(
         &mut self,
         bundle: &str,
@@ -402,14 +409,21 @@ impl BundleStore {
         for mut entry in entries {
             let key = entry.effective_key().to_string();
             let mut previously_owned = false;
+            let mut prior_user_origin = false;
             for record in self.bundles.values_mut() {
                 let before = record.mcp_servers.len();
-                record
-                    .mcp_servers
-                    .retain(|owned| owned.effective_key() != key);
+                record.mcp_servers.retain(|owned| {
+                    if owned.effective_key() != key {
+                        return true;
+                    }
+                    if owned.action == McpAction::Replaced {
+                        prior_user_origin = true;
+                    }
+                    false
+                });
                 previously_owned |= record.mcp_servers.len() != before;
             }
-            if previously_owned && entry.action == McpAction::Replaced {
+            if previously_owned && !prior_user_origin && entry.action == McpAction::Replaced {
                 entry.action = McpAction::Transferred;
             }
             self.bundles
@@ -852,6 +866,64 @@ mod tests {
         assert_eq!(servers[0].sha256.as_deref(), Some("deadbeef"));
     }
 
+    #[test]
+    fn mcp_rerecord_of_own_replaced_entry_stays_replaced() {
+        let dir = TempStoreDir::new("bundles-mcp-sticky-self");
+        let mut store = dir.store();
+        store
+            .upsert_bundle("omc", metadata("https://github.com/x/omc", "abc123"))
+            .unwrap();
+        store
+            .record_mcp_servers(
+                "omc",
+                vec![mcp_record("user-srv", McpAction::Replaced, None)],
+            )
+            .unwrap();
+
+        store
+            .record_mcp_servers(
+                "omc",
+                vec![mcp_record("user-srv", McpAction::Replaced, None)],
+            )
+            .unwrap();
+
+        assert_eq!(
+            store.get("omc").unwrap().mcp_servers[0].action,
+            McpAction::Replaced
+        );
+    }
+
+    #[test]
+    fn mcp_transfer_of_replaced_entry_keeps_user_origin_marker() {
+        let dir = TempStoreDir::new("bundles-mcp-sticky-transfer");
+        let mut store = dir.store();
+        store
+            .upsert_bundle("alpha", metadata("https://github.com/a/alpha", "abc123"))
+            .unwrap();
+        store
+            .upsert_bundle("beta", metadata("https://github.com/b/beta", "def456"))
+            .unwrap();
+        store
+            .record_mcp_servers(
+                "alpha",
+                vec![mcp_record("user-srv", McpAction::Replaced, None)],
+            )
+            .unwrap();
+
+        store
+            .record_mcp_servers(
+                "beta",
+                vec![mcp_record("user-srv", McpAction::Replaced, None)],
+            )
+            .unwrap();
+
+        assert!(store.get("alpha").unwrap().mcp_servers.is_empty());
+        assert_eq!(
+            store.get("beta").unwrap().mcp_servers[0].action,
+            McpAction::Replaced
+        );
+    }
+
     #[test]
     fn mcp_transfer_matches_renamed_entries_by_effective_key() {
         let dir = TempStoreDir::new("bundles-mcp-renamed");
@@ -893,7 +965,7 @@ mod tests {
             .unwrap();
 
         let resolved = store
-            .resolve_bundle_name("git@github.com:X/omc.git", None)
+            .resolve_bundle_name("git@github.com:x/omc.git", None)
             .unwrap();
 
         assert_eq!(resolved.name, "omc");

src/config/install_remote.rs

@@ -151,7 +151,7 @@ fn looks_like_remote_source(value: &str) -> bool {
     }
 }
 
-const DEFAULT_GIT_HOST: &str = "github.com";
+pub(crate) const DEFAULT_GIT_HOST: &str = "github.com";
 
 fn is_repo_shorthand(value: &str) -> bool {
     let path = strip_ref_suffix(value);
@@ -174,7 +174,7 @@ fn expand_repo_shorthand(value: &str, git_host: Option<&str>) -> Result<String>
         .or_else(|| raw.strip_prefix("http://"))
         .unwrap_or(raw)
         .trim_matches('/');
-    if host.is_empty() || host.contains('/') || host.chars().any(char::is_whitespace) {
+    if host.is_empty() || host.contains(['/', '#', '?']) || host.chars().any(char::is_whitespace) {
         bail!("invalid --git-host '{raw}': expected a bare host like git.somedomain.com");
     }
     Ok(format!("https://{host}/{value}"))
@@ -951,12 +951,18 @@ fn clone_to_temp(url: &str, reference: Option<&str>) -> Result<TempRepoDir> {
                 "1".into(),
                 "--branch".into(),
                 r.into(),
+                "--".into(),
                 url.into(),
                 dest_arg,
             ])?;
         }
         Some(r) => {
-            run_git(vec!["clone".into(), url.into(), dest_arg.clone()])?;
+            run_git(vec![
+                "clone".into(),
+                "--".into(),
+                url.into(),
+                dest_arg.clone(),
+            ])?;
             run_git(vec!["-C".into(), dest_arg, "checkout".into(), r.into()])?;
         }
         None => {
@@ -964,6 +970,7 @@ fn clone_to_temp(url: &str, reference: Option<&str>) -> Result<TempRepoDir> {
                 "clone".into(),
                 "--depth".into(),
                 "1".into(),
+                "--".into(),
                 url.into(),
                 dest_arg,
             ])?;
@@ -1223,14 +1230,17 @@ fn sanitize_host(host: &str) -> String {
         .to_string()
 }
 
+/// The host compares case-insensitively but the path keeps its case: many
+/// self-hosted forges treat repository paths as case-sensitive, and collapsing
+/// distinct repos into one record misdirects updates and uninstalls.
 pub(crate) fn canonical_source_url(url: &str) -> String {
     let (host, path) = split_host_and_path(url);
-    let mut path = path.to_ascii_lowercase();
-    if let Some(stripped) = path.strip_suffix(".git")
-        && !stripped.is_empty()
-        && !stripped.ends_with('/')
-    {
-        path = stripped.to_string();
+    let mut path = path;
+    if path.to_ascii_lowercase().ends_with(".git") {
+        let stripped = &path[..path.len() - 4];
+        if !stripped.is_empty() && !stripped.ends_with('/') {
+            path.truncate(path.len() - 4);
+        }
     }
     let host = host.to_ascii_lowercase();
     if host.is_empty() {
@@ -2837,10 +2847,14 @@ mod tests {
     }
 
     #[test]
-    fn canonical_source_url_lowercases_host_and_path() {
+    fn canonical_source_url_lowercases_host_but_not_path() {
         assert_eq!(
             canonical_source_url("https://GitHub.COM/X/R.git"),
-            "github.com/x/r"
+            "github.com/X/R"
+        );
+        assert_ne!(
+            canonical_source_url("https://gitlab.example.com/team/Repo"),
+            canonical_source_url("https://gitlab.example.com/team/repo")
         );
     }
 

src/config/request_context.rs

@@ -3501,7 +3501,9 @@ impl RequestContext {
                     InstallFilter::NAMES.iter().map(|s| s.to_string()).collect(),
                 );
             } else if prev == "--git-host" {
-                values = super::map_completion_values(vec!["github.com".to_string()]);
+                values = super::map_completion_values(vec![
+                    super::install_remote::DEFAULT_GIT_HOST.to_string(),
+                ]);
             } else {
                 let has_filter = args.iter().enumerate().any(|(i, a)| {
                     a.starts_with("--filter=") || (*a == "--filter" && i < args.len() - 1)

src/function/mod.rs

@@ -165,7 +165,16 @@ pub(crate) fn write_file_atomic(
         std::process::id(),
         TMP_COUNTER.fetch_add(1, Ordering::Relaxed)
     ));
-    fs::write(&tmp, content)?;
+    let write_synced = || -> std::io::Result<()> {
+        use std::io::Write;
+        let mut file = fs::File::create(&tmp)?;
+        file.write_all(content.as_bytes())?;
+        file.sync_all()
+    };
+    if let Err(err) = write_synced() {
+        let _ = fs::remove_file(&tmp);
+        return Err(err.into());
+    }
 
     #[cfg(unix)]
     if let Some(mode) = mode {

src/main.rs

@@ -107,7 +107,6 @@ async fn main() -> Result<()> {
         || cli.list_rags
         || cli.list_macros
         || cli.list_skills
-        || cli.list_bundles
         || cli.list_sessions;
     let vault_flags = cli.add_secret.is_some()
         || cli.get_secret.is_some()
@@ -128,6 +127,10 @@ async fn main() -> Result<()> {
         return sandbox::launch(name.clone(), cli.fresh);
     }
 
+    if cli.install_from.is_some() {
+        bail!("--install-from was removed; use --install <GIT_URL|OWNER/REPO> instead");
+    }
+
     install_builtins()?;
 
     if let Some(category) = cli.install_builtins {
@@ -151,6 +154,10 @@ async fn main() -> Result<()> {
         return config::uninstall_bundle(name, cli.yes);
     }
 
+    if cli.list_bundles {
+        return config::list_installed_bundles();
+    }
+
     if let Some(client_arg) = &cli.authenticate {
         let cfg = Config::load_with_interpolation(true).await?;
         let app_config = AppConfig::from_config(cfg)?;
@@ -323,9 +330,6 @@ async fn run(
         println!("{skills}");
         return Ok(());
     }
-    if cli.list_bundles {
-        return config::list_installed_bundles();
-    }
     let skills = cli.skills();
     if skills.len() == 1 {
         let name = &skills[0];

src/repl/mod.rs

@@ -875,6 +875,9 @@ pub async fn run_repl_command(
                 ReplInstallDispatch::Unified(value) => {
                     config::install_or_update_from_repl_args(value)?;
                 }
+                ReplInstallDispatch::RemovedRemote => println!(
+                    "'.install remote <git-url>' was removed; use '.install <git-url>' directly."
+                ),
                 ReplInstallDispatch::Usage => println!(
                     "Usage: .install <{}> | .install <git-url|owner/repo|installed-bundle> \
                          [--git-host <host>] [--filter <cat>] [--force]",
@@ -1197,12 +1200,20 @@ pub async fn run_repl_command(
                     println!("Usage: .delete <role|session|rag|macro|skill|agent-data>")
                 }
             },
-            ".uninstall" => match args {
-                Some(args) => {
-                    config::uninstall_bundle(args.trim(), false)?;
+            ".uninstall" => {
+                let mut assume_yes = false;
+                let mut names = Vec::new();
+                for token in args.unwrap_or("").split_whitespace() {
+                    match token {
+                        "--yes" | "-y" => assume_yes = true,
+                        other => names.push(other),
+                    }
                 }
-                _ => println!("Usage: .uninstall <bundle-name>"),
-            },
+                match names.as_slice() {
+                    [name] => config::uninstall_bundle(name, assume_yes)?,
+                    _ => println!("Usage: .uninstall <bundle-name> [--yes]"),
+                }
+            }
             ".list" => match args {
                 Some(args) => {
                     ctx.list_assets(args.trim())?;
@@ -1575,6 +1586,7 @@ fn unknown_command() -> Result<()> {
 enum ReplInstallDispatch<'a> {
     Builtins(AssetCategory),
     Unified(&'a str),
+    RemovedRemote,
     Usage,
 }
 
@@ -1582,10 +1594,15 @@ fn parse_repl_install(args: Option<&str>) -> ReplInstallDispatch<'_> {
     let trimmed = args.map(str::trim).unwrap_or("");
     let mut parts = trimmed.splitn(2, char::is_whitespace);
     match parts.next() {
-        Some(name) if !name.is_empty() => match AssetCategory::parse(name) {
-            Some(category) => ReplInstallDispatch::Builtins(category),
-            None => ReplInstallDispatch::Unified(trimmed),
-        },
+        Some(name) if !name.is_empty() => {
+            let rest = parts.next().map(str::trim).unwrap_or("");
+            match AssetCategory::parse(name) {
+                Some(category) if rest.is_empty() => ReplInstallDispatch::Builtins(category),
+                Some(_) => ReplInstallDispatch::Usage,
+                None if name == "remote" && !rest.is_empty() => ReplInstallDispatch::RemovedRemote,
+                None => ReplInstallDispatch::Unified(trimmed),
+            }
+        }
         _ => ReplInstallDispatch::Usage,
     }
 }
@@ -1841,6 +1858,30 @@ mod tests {
         assert_eq!(parse_repl_install(Some("  ")), ReplInstallDispatch::Usage);
     }
 
+    #[test]
+    fn parse_repl_install_rejects_extra_tokens_after_a_category() {
+        assert_eq!(
+            parse_repl_install(Some("agents --force")),
+            ReplInstallDispatch::Usage
+        );
+        assert_eq!(
+            parse_repl_install(Some("agents extra")),
+            ReplInstallDispatch::Usage
+        );
+    }
+
+    #[test]
+    fn parse_repl_install_hints_on_removed_remote_form() {
+        assert_eq!(
+            parse_repl_install(Some("remote https://github.com/x/y")),
+            ReplInstallDispatch::RemovedRemote
+        );
+        assert_eq!(
+            parse_repl_install(Some("remote")),
+            ReplInstallDispatch::Unified("remote")
+        );
+    }
+
     #[test]
     fn builtin_command_names_are_sorted_deduped_first_words_without_dots() {
         let names = builtin_command_names();