diff --git a/src/config/install_remote.rs b/src/config/install_remote.rs
index 5013171..84c9d9e 100644
--- a/src/config/install_remote.rs
+++ b/src/config/install_remote.rs
@@ -4790,6 +4790,49 @@ mod tests {
         let _ = fs::remove_dir_all(&dir);
     }
 
+    #[test]
+    fn uninstall_mcp_preserves_allowed_tools_on_surviving_entries() {
+        let dir = fresh_temp_dir("uninst-mcp-allowed-tools-");
+        let mut store = BundleStore::load_from(dir.join("installed-bundles.yaml")).unwrap();
+        store
+            .upsert_bundle("omc", test_metadata("https://github.com/x/omc"))
+            .unwrap();
+        let mcp = dir.join("mcp.json");
+        write_mcp(
+            &mcp,
+            r#"{"mcpServers": {
+                "srv": {"type": "stdio", "command": "echo"},
+                "user-srv": {"type": "stdio", "command": "mine", "allowedTools": ["get_*", "list_issues"]}
+            }}"#,
+        );
+        let parsed: McpServersConfig =
+            serde_json::from_str(&fs::read_to_string(&mcp).unwrap()).unwrap();
+        let hash = hash_bytes(
+            serde_json::to_string(parsed.mcp_servers.get("srv").unwrap())
+                .unwrap()
+                .as_bytes(),
+        );
+        store
+            .record_mcp_servers(
+                "omc",
+                vec![mcp_server_record("srv", McpAction::Added, Some(hash))],
+            )
+            .unwrap();
+        let servers = store.get("omc").unwrap().mcp_servers.clone();
+
+        let summary = uninstall_mcp_entries(&mut store, "omc", &servers, &mcp, true).unwrap();
+
+        assert_eq!(summary.removed, vec!["srv"]);
+        let raw = fs::read_to_string(&mcp).unwrap();
+        assert!(raw.contains("allowedTools"));
+        let written: McpServersConfig = serde_json::from_str(&raw).unwrap();
+        assert_eq!(
+            written.mcp_servers.get("user-srv").unwrap().allowed_tools,
+            Some(vec!["get_*".to_string(), "list_issues".to_string()])
+        );
+        let _ = fs::remove_dir_all(&dir);
+    }
+
     #[test]
     fn uninstall_mcp_reports_referenced_secrets_without_removing_them() {
         let dir = fresh_temp_dir("uninst-mcp-secrets-");
diff --git a/src/config/mcp_factory.rs b/src/config/mcp_factory.rs
index 961847d..23dba66 100644
--- a/src/config/mcp_factory.rs
+++ b/src/config/mcp_factory.rs
@@ -139,6 +139,7 @@ mod tests {
             url: None,
             headers: None,
             oauth: None,
+            allowed_tools: None,
         }
     }
 
@@ -156,6 +157,7 @@ mod tests {
             url: Some(url.to_string()),
             headers,
             oauth: None,
+            allowed_tools: None,
         }
     }
 
diff --git a/src/config/mcp_tool_policy.rs b/src/config/mcp_tool_policy.rs
new file mode 100644
index 0000000..48581b1
--- /dev/null
+++ b/src/config/mcp_tool_policy.rs
@@ -0,0 +1,759 @@
+use crate::mcp::McpServersConfig;
+
+use fancy_regex::Regex;
+use indexmap::IndexMap;
+use log::warn;
+use std::collections::HashMap;
+use std::fmt;
+
+/// The configuration level that contributed a layer of tool patterns for an
+/// MCP server, as rendered in diagnostics.
+#[allow(dead_code)]
+#[derive(Debug, Clone, PartialEq, Eq)]
+pub enum LayerSource {
+    Global,
+    AppConfig,
+    Role(String),
+    Agent(String),
+    Session,
+    Skill(String),
+    Node(String),
+}
+
+impl fmt::Display for LayerSource {
+    fn fmt(&self, f: &mut fmt::Formatter<'_>) -> fmt::Result {
+        match self {
+            LayerSource::Global => write!(f, "global (mcp.json)"),
+            LayerSource::AppConfig => write!(f, "config (config.yaml)"),
+            LayerSource::Role(name) => write!(f, "role ({name})"),
+            LayerSource::Agent(name) => write!(f, "agent ({name})"),
+            LayerSource::Session => write!(f, "session (.set)"),
+            LayerSource::Skill(name) => write!(f, "skill ({name})"),
+            LayerSource::Node(id) => write!(f, "node ({id})"),
+        }
+    }
+}
+
+#[allow(dead_code)]
+#[derive(Debug)]
+pub struct CompiledPatterns {
+    source: LayerSource,
+    raw: Vec<String>,
+    regexes: Vec<Regex>,
+}
+
+#[allow(dead_code)]
+#[derive(Debug, Default)]
+pub struct ToolFilter {
+    layers: Vec<CompiledPatterns>,
+}
+
+#[allow(dead_code)]
+impl ToolFilter {
+    pub fn push_layer(&mut self, source: LayerSource, patterns: &[String]) {
+        self.layers.push(CompiledPatterns {
+            source,
+            raw: patterns.to_vec(),
+            regexes: patterns.iter().map(|p| compile_glob(p)).collect(),
+        });
+    }
+
+    /// A tool is allowed iff it matches at least one pattern in every layer.
+    pub fn allows(&self, tool: &str) -> bool {
+        self.layers.iter().all(|layer| {
+            layer
+                .regexes
+                .iter()
+                .any(|regex| regex.is_match(tool).unwrap_or(false))
+        })
+    }
+
+    /// The first matching raw pattern per layer, in layer order, or the
+    /// source of the first layer with no match.
+    pub fn allows_explain(&self, tool: &str) -> Result<Vec<(&LayerSource, &str)>, &LayerSource> {
+        let mut matched = Vec::with_capacity(self.layers.len());
+        for layer in &self.layers {
+            // fancy_regex can fail at match time (backtracking limits);
+            // treat that as a non-match rather than allowing the tool.
+            match layer
+                .regexes
+                .iter()
+                .position(|regex| regex.is_match(tool).unwrap_or(false))
+            {
+                Some(index) => matched.push((&layer.source, layer.raw[index].as_str())),
+                None => return Err(&layer.source),
+            }
+        }
+        Ok(matched)
+    }
+}
+
+/// Translates a glob pattern (`*` = any run of characters, `?` = exactly one)
+/// into an anchored regex. Patterns that fail to compile match nothing.
+#[allow(dead_code)]
+fn compile_glob(pattern: &str) -> Regex {
+    let translated = format!(
+        "^{}$",
+        fancy_regex::escape(pattern)
+            .replace("\\*", ".*")
+            .replace("\\?", ".")
+    );
+    Regex::new(&translated).unwrap_or_else(|error| {
+        warn!("Invalid MCP tool pattern '{pattern}': {error}. It will match nothing.");
+        never_matching_regex()
+    })
+}
+
+#[allow(dead_code)]
+fn never_matching_regex() -> Regex {
+    Regex::new("(?!)").expect("'(?!)' is a valid never-matching regex")
+}
+
+#[allow(dead_code)]
+pub struct SkillMcpLayer {
+    pub name: String,
+    pub enabled_servers: Vec<String>,
+    pub mcp_tools: IndexMap<String, Vec<String>>,
+}
+
+#[allow(dead_code)]
+pub struct McpToolPolicy;
+
+#[allow(dead_code)]
+impl McpToolPolicy {
+    #[allow(clippy::too_many_arguments)]
+    pub fn effective(
+        mcp_config: &McpServersConfig,
+        session: Option<&IndexMap<String, Vec<String>>>,
+        agent: Option<(&str, &IndexMap<String, Vec<String>>)>,
+        role: Option<(&str, &IndexMap<String, Vec<String>>)>,
+        global: Option<&IndexMap<String, Vec<String>>>,
+        skills: &[SkillMcpLayer],
+        node: Option<(&str, &IndexMap<String, Vec<String>>)>,
+        aliases: &IndexMap<String, String>,
+    ) -> HashMap<String, ToolFilter> {
+        let mut filters: HashMap<String, ToolFilter> = HashMap::new();
+
+        for (server, spec) in &mcp_config.mcp_servers {
+            if let Some(patterns) = &spec.allowed_tools {
+                filters
+                    .entry(server.clone())
+                    .or_default()
+                    .push_layer(LayerSource::Global, patterns);
+            }
+        }
+
+        if let Some(map) = global {
+            push_level(
+                &mut filters,
+                mcp_config,
+                aliases,
+                &LayerSource::AppConfig,
+                map,
+                None,
+            );
+        }
+        if let Some((name, map)) = role {
+            push_level(
+                &mut filters,
+                mcp_config,
+                aliases,
+                &LayerSource::Role(name.to_string()),
+                map,
+                None,
+            );
+        }
+        if let Some((name, map)) = agent {
+            push_level(
+                &mut filters,
+                mcp_config,
+                aliases,
+                &LayerSource::Agent(name.to_string()),
+                map,
+                None,
+            );
+        }
+        if let Some(map) = session {
+            push_level(
+                &mut filters,
+                mcp_config,
+                aliases,
+                &LayerSource::Session,
+                map,
+                None,
+            );
+        }
+        for skill in skills {
+            push_level(
+                &mut filters,
+                mcp_config,
+                aliases,
+                &LayerSource::Skill(skill.name.clone()),
+                &skill.mcp_tools,
+                Some(&skill.enabled_servers),
+            );
+        }
+        if let Some((id, map)) = node {
+            push_level(
+                &mut filters,
+                mcp_config,
+                aliases,
+                &LayerSource::Node(id.to_string()),
+                map,
+                None,
+            );
+        }
+
+        filters
+    }
+}
+
+#[allow(dead_code)]
+fn push_level(
+    filters: &mut HashMap<String, ToolFilter>,
+    mcp_config: &McpServersConfig,
+    aliases: &IndexMap<String, String>,
+    source: &LayerSource,
+    map: &IndexMap<String, Vec<String>>,
+    enabled_servers: Option<&[String]>,
+) {
+    for (server, patterns) in expand_server_keys(mcp_config, aliases, map) {
+        if let Some(enabled) = enabled_servers
+            && !enabled.iter().any(|id| id == &server)
+        {
+            continue;
+        }
+        filters
+            .entry(server)
+            .or_default()
+            .push_layer(source.clone(), &patterns);
+    }
+}
+
+/// Expands map keys to server ids: a key that is a server id maps to itself;
+/// a key that is an alias expands to every configured id in its
+/// comma-separated value; anything else is dropped. Keys expanding to the
+/// same server merge their pattern lists.
+#[allow(dead_code)]
+fn expand_server_keys(
+    mcp_config: &McpServersConfig,
+    aliases: &IndexMap<String, String>,
+    map: &IndexMap<String, Vec<String>>,
+) -> IndexMap<String, Vec<String>> {
+    let mut expanded: IndexMap<String, Vec<String>> = IndexMap::new();
+    for (key, patterns) in map {
+        let key = key.trim();
+        if mcp_config.mcp_servers.contains_key(key) {
+            expanded
+                .entry(key.to_string())
+                .or_default()
+                .extend(patterns.iter().cloned());
+        } else if let Some(mapped) = aliases.get(key) {
+            for mapped_id in mapped.split(',').map(str::trim) {
+                if mcp_config.mcp_servers.contains_key(mapped_id) {
+                    expanded
+                        .entry(mapped_id.to_string())
+                        .or_default()
+                        .extend(patterns.iter().cloned());
+                }
+            }
+        }
+    }
+    expanded
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+    use crate::mcp::{McpServer, McpServersConfig, McpTransportType};
+
+    fn spec(allowed_tools: Option<&[&str]>) -> McpServer {
+        McpServer {
+            transport_type: McpTransportType::Stdio,
+            command: Some("echo".to_string()),
+            args: None,
+            env: None,
+            cwd: None,
+            url: None,
+            headers: None,
+            oauth: None,
+            allowed_tools: allowed_tools.map(list),
+        }
+    }
+
+    fn config(servers: &[(&str, Option<&[&str]>)]) -> McpServersConfig {
+        McpServersConfig {
+            mcp_servers: servers
+                .iter()
+                .map(|(name, tools)| (name.to_string(), spec(*tools)))
+                .collect(),
+        }
+    }
+
+    fn list(items: &[&str]) -> Vec<String> {
+        items.iter().map(|s| s.to_string()).collect()
+    }
+
+    fn tool_map(entries: &[(&str, &[&str])]) -> IndexMap<String, Vec<String>> {
+        entries
+            .iter()
+            .map(|(server, patterns)| (server.to_string(), list(patterns)))
+            .collect()
+    }
+
+    fn single_layer(patterns: &[&str]) -> ToolFilter {
+        layered(&[(LayerSource::Global, patterns)])
+    }
+
+    fn layered(layers: &[(LayerSource, &[&str])]) -> ToolFilter {
+        let mut filter = ToolFilter::default();
+        for (source, patterns) in layers {
+            filter.push_layer(source.clone(), &list(patterns));
+        }
+        filter
+    }
+
+    fn no_aliases() -> IndexMap<String, String> {
+        IndexMap::new()
+    }
+
+    fn aliases(entries: &[(&str, &str)]) -> IndexMap<String, String> {
+        entries
+            .iter()
+            .map(|(key, value)| (key.to_string(), value.to_string()))
+            .collect()
+    }
+
+    fn resolve(
+        config: &McpServersConfig,
+        session: Option<&IndexMap<String, Vec<String>>>,
+        role: Option<(&str, &IndexMap<String, Vec<String>>)>,
+    ) -> HashMap<String, ToolFilter> {
+        McpToolPolicy::effective(config, session, None, role, None, &[], None, &no_aliases())
+    }
+
+    #[test]
+    fn literal_pattern_matches_only_the_exact_name() {
+        let filter = single_layer(&["get_issue"]);
+
+        assert!(filter.allows("get_issue"));
+        assert!(!filter.allows("get_issues"));
+        assert!(!filter.allows("get_issu"));
+        assert!(!filter.allows("xget_issue"));
+    }
+
+    #[test]
+    fn star_matches_any_run_of_characters() {
+        let filter = single_layer(&["get_*"]);
+        assert!(filter.allows("get_issue"));
+        assert!(filter.allows("get_"));
+        assert!(!filter.allows("set_issue"));
+
+        let filter = single_layer(&["*_issue"]);
+        assert!(filter.allows("create_issue"));
+        assert!(!filter.allows("create_pr"));
+
+        let filter = single_layer(&["get*sue"]);
+        assert!(filter.allows("get_issue"));
+        assert!(filter.allows("getsue"));
+
+        let filter = single_layer(&["*"]);
+        assert!(filter.allows(""));
+        assert!(filter.allows("anything_at_all"));
+    }
+
+    #[test]
+    fn question_mark_matches_exactly_one_character() {
+        let filter = single_layer(&["get_?"]);
+
+        assert!(filter.allows("get_a"));
+        assert!(!filter.allows("get_"));
+        assert!(!filter.allows("get_ab"));
+    }
+
+    #[test]
+    fn regex_metacharacters_are_matched_literally() {
+        let filter = single_layer(&["get.issue"]);
+        assert!(filter.allows("get.issue"));
+        assert!(!filter.allows("getXissue"));
+
+        for pattern in ["a(b", "a[b", "a+b", "a|b", "a$b"] {
+            let filter = single_layer(&[pattern]);
+            assert!(filter.allows(pattern), "'{pattern}' should match itself");
+            assert!(!filter.allows("ab"), "'{pattern}' should not match 'ab'");
+        }
+    }
+
+    #[test]
+    fn backslash_is_literal_and_star_still_wildcards() {
+        let filter = single_layer(&["a\\b"]);
+        assert!(filter.allows("a\\b"));
+        assert!(!filter.allows("ab"));
+
+        let filter = single_layer(&["a\\*b"]);
+        assert!(filter.allows("a\\b"));
+        assert!(filter.allows("a\\xyzb"));
+        assert!(!filter.allows("ab"));
+    }
+
+    #[test]
+    fn the_never_matching_placeholder_matches_nothing() {
+        let regex = never_matching_regex();
+
+        assert!(!regex.is_match("").unwrap());
+        assert!(!regex.is_match("anything").unwrap());
+    }
+
+    #[test]
+    fn within_a_layer_any_pattern_may_match() {
+        let filter = single_layer(&["get_*", "set_*"]);
+
+        assert!(filter.allows("get_x"));
+        assert!(filter.allows("set_x"));
+        assert!(!filter.allows("delete_x"));
+    }
+
+    #[test]
+    fn across_layers_every_layer_must_match() {
+        let filter = layered(&[
+            (LayerSource::Global, &["get_*"]),
+            (LayerSource::Session, &["*_issue"]),
+        ]);
+
+        assert!(filter.allows("get_issue"));
+        assert!(!filter.allows("get_pr"));
+        assert!(!filter.allows("create_issue"));
+    }
+
+    #[test]
+    fn an_empty_layer_blocks_everything() {
+        let filter = layered(&[(LayerSource::Global, &["*"]), (LayerSource::Session, &[])]);
+
+        assert!(!filter.allows("anything"));
+        assert_eq!(
+            filter.allows_explain("anything"),
+            Err(&LayerSource::Session)
+        );
+    }
+
+    #[test]
+    fn allows_explain_reports_the_first_matching_pattern_per_layer() {
+        let filter = layered(&[
+            (LayerSource::Global, &["x_*", "get_*"]),
+            (LayerSource::Session, &["*"]),
+        ]);
+
+        assert_eq!(
+            filter.allows_explain("get_issue").unwrap(),
+            vec![
+                (&LayerSource::Global, "get_*"),
+                (&LayerSource::Session, "*")
+            ]
+        );
+    }
+
+    #[test]
+    fn allows_explain_reports_the_first_layer_without_a_match() {
+        let filter = layered(&[
+            (LayerSource::Global, &["get_*"]),
+            (LayerSource::Session, &["*"]),
+        ]);
+        assert_eq!(
+            filter.allows_explain("delete_repo"),
+            Err(&LayerSource::Global)
+        );
+
+        let filter = layered(&[
+            (LayerSource::Global, &["*"]),
+            (LayerSource::Session, &["get_*"]),
+        ]);
+        assert_eq!(
+            filter.allows_explain("delete_repo"),
+            Err(&LayerSource::Session)
+        );
+    }
+
+    #[test]
+    fn global_allowed_tools_from_mcp_json_is_the_first_layer() {
+        let config = config(&[("gh", Some(&["get_*"]))]);
+        let session_map = tool_map(&[("gh", &["*"])]);
+
+        let filters = resolve(&config, Some(&session_map), None);
+
+        assert_eq!(
+            filters["gh"].allows_explain("get_issue").unwrap(),
+            vec![
+                (&LayerSource::Global, "get_*"),
+                (&LayerSource::Session, "*")
+            ]
+        );
+    }
+
+    #[test]
+    fn servers_without_patterns_at_any_level_are_absent() {
+        let config = config(&[("gh", None)]);
+
+        let filters = resolve(&config, None, None);
+
+        assert!(filters.is_empty());
+    }
+
+    #[test]
+    fn server_absent_from_a_level_map_gets_no_layer_from_it() {
+        let config = config(&[("gh", Some(&["get_*"])), ("gl", None)]);
+        let role_map = tool_map(&[("gl", &["x_*"])]);
+
+        let filters = resolve(&config, None, Some(("dev", &role_map)));
+
+        assert!(filters["gh"].allows("get_issue"));
+        assert!(!filters["gh"].allows("delete_repo"));
+        assert_eq!(filters["gh"].allows_explain("get_issue").unwrap().len(), 1);
+        assert!(filters["gl"].allows("x_1"));
+        assert!(!filters["gl"].allows("y_1"));
+    }
+
+    #[test]
+    fn empty_pattern_list_at_a_level_blocks_all_tools_for_that_server() {
+        let config = config(&[("gh", Some(&["get_*"]))]);
+        let session_map = tool_map(&[("gh", &[])]);
+
+        let filters = resolve(&config, Some(&session_map), None);
+
+        assert!(!filters["gh"].allows("get_issue"));
+        assert_eq!(
+            filters["gh"].allows_explain("get_issue"),
+            Err(&LayerSource::Session)
+        );
+    }
+
+    #[test]
+    fn session_cannot_widen_a_role_restriction() {
+        let config = config(&[("gh", None)]);
+        let role_map = tool_map(&[("gh", &["get_*"])]);
+        let session_map = tool_map(&[("gh", &["*"])]);
+
+        let filters = resolve(&config, Some(&session_map), Some(("dev", &role_map)));
+
+        assert!(filters["gh"].allows("get_issue"));
+        assert!(!filters["gh"].allows("delete_repo"));
+    }
+
+    #[test]
+    fn app_config_map_contributes_its_own_layer() {
+        let config = config(&[("gh", None)]);
+        let app_map = tool_map(&[("gh", &["get_*"])]);
+
+        let filters = McpToolPolicy::effective(
+            &config,
+            None,
+            None,
+            None,
+            Some(&app_map),
+            &[],
+            None,
+            &no_aliases(),
+        );
+
+        assert_eq!(
+            filters["gh"].allows_explain("get_issue").unwrap(),
+            vec![(&LayerSource::AppConfig, "get_*")]
+        );
+        assert!(!filters["gh"].allows("delete_repo"));
+    }
+
+    #[test]
+    fn skill_layer_applies_only_to_its_enabled_servers() {
+        let config = config(&[("gh", None), ("gl", None)]);
+        let skill = SkillMcpLayer {
+            name: "reviewer".to_string(),
+            enabled_servers: vec!["gh".to_string()],
+            mcp_tools: tool_map(&[("gh", &["get_*"]), ("gl", &["*"])]),
+        };
+
+        let filters = McpToolPolicy::effective(
+            &config,
+            None,
+            None,
+            None,
+            None,
+            &[skill],
+            None,
+            &no_aliases(),
+        );
+
+        assert!(filters.contains_key("gh"));
+        assert!(!filters.contains_key("gl"));
+    }
+
+    #[test]
+    fn two_skills_naming_the_same_server_stack_independent_layers() {
+        let config = config(&[("gh", None)]);
+        let skills = vec![
+            SkillMcpLayer {
+                name: "a".to_string(),
+                enabled_servers: vec!["gh".to_string()],
+                mcp_tools: tool_map(&[("gh", &["get_*"])]),
+            },
+            SkillMcpLayer {
+                name: "b".to_string(),
+                enabled_servers: vec!["gh".to_string()],
+                mcp_tools: tool_map(&[("gh", &["*_issue"])]),
+            },
+        ];
+
+        let filters = McpToolPolicy::effective(
+            &config,
+            None,
+            None,
+            None,
+            None,
+            &skills,
+            None,
+            &no_aliases(),
+        );
+
+        assert!(filters["gh"].allows("get_issue"));
+        assert!(!filters["gh"].allows("get_pr"));
+        assert!(!filters["gh"].allows("create_issue"));
+        assert_eq!(filters["gh"].allows_explain("get_issue").unwrap().len(), 2);
+    }
+
+    #[test]
+    fn layers_stack_in_documented_order_with_node_last() {
+        let config = config(&[("gh", Some(&["*"]))]);
+        let app_map = tool_map(&[("gh", &["*"])]);
+        let role_map = tool_map(&[("gh", &["*"])]);
+        let agent_map = tool_map(&[("gh", &["*"])]);
+        let session_map = tool_map(&[("gh", &["*"])]);
+        let skills = vec![SkillMcpLayer {
+            name: "reviewer".to_string(),
+            enabled_servers: vec!["gh".to_string()],
+            mcp_tools: tool_map(&[("gh", &["*"])]),
+        }];
+        let node_map = tool_map(&[("gh", &["*"])]);
+
+        let filters = McpToolPolicy::effective(
+            &config,
+            Some(&session_map),
+            Some(("worker", &agent_map)),
+            Some(("dev", &role_map)),
+            Some(&app_map),
+            &skills,
+            Some(("n1", &node_map)),
+            &no_aliases(),
+        );
+
+        let sources: Vec<String> = filters["gh"]
+            .allows_explain("anything")
+            .unwrap()
+            .iter()
+            .map(|(source, _)| source.to_string())
+            .collect();
+        assert_eq!(
+            sources,
+            vec![
+                "global (mcp.json)",
+                "config (config.yaml)",
+                "role (dev)",
+                "agent (worker)",
+                "session (.set)",
+                "skill (reviewer)",
+                "node (n1)",
+            ]
+        );
+    }
+
+    #[test]
+    fn alias_key_expands_to_all_mapped_servers() {
+        let config = config(&[("github", None), ("gitlab", None)]);
+        let role_map = tool_map(&[("gh", &["get_*"])]);
+
+        let filters = McpToolPolicy::effective(
+            &config,
+            None,
+            None,
+            Some(("dev", &role_map)),
+            None,
+            &[],
+            None,
+            &aliases(&[("gh", "github,gitlab")]),
+        );
+
+        assert!(filters["github"].allows("get_issue"));
+        assert!(!filters["github"].allows("delete_repo"));
+        assert!(filters["gitlab"].allows("get_issue"));
+        assert!(!filters["gitlab"].allows("delete_repo"));
+    }
+
+    #[test]
+    fn alias_ids_missing_from_the_config_are_skipped() {
+        let config = config(&[("github", None)]);
+        let role_map = tool_map(&[("gh", &["get_*"])]);
+
+        let filters = McpToolPolicy::effective(
+            &config,
+            None,
+            None,
+            Some(("dev", &role_map)),
+            None,
+            &[],
+            None,
+            &aliases(&[("gh", "github,missing")]),
+        );
+
+        assert_eq!(filters.len(), 1);
+        assert!(filters.contains_key("github"));
+    }
+
+    #[test]
+    fn unknown_map_keys_are_dropped() {
+        let config = config(&[("github", None)]);
+        let role_map = tool_map(&[("nope", &["get_*"])]);
+
+        let filters = resolve(&config, None, Some(("dev", &role_map)));
+
+        assert!(filters.is_empty());
+    }
+
+    #[test]
+    fn alias_and_direct_key_for_the_same_server_merge_into_one_layer() {
+        let config = config(&[("github", None)]);
+        let role_map = tool_map(&[("gh", &["get_*"]), ("github", &["set_*"])]);
+
+        let filters = McpToolPolicy::effective(
+            &config,
+            None,
+            None,
+            Some(("dev", &role_map)),
+            None,
+            &[],
+            None,
+            &aliases(&[("gh", "github")]),
+        );
+
+        assert!(filters["github"].allows("get_issue"));
+        assert!(filters["github"].allows("set_topic"));
+        assert!(!filters["github"].allows("delete_repo"));
+        assert_eq!(
+            filters["github"].allows_explain("get_issue").unwrap().len(),
+            1
+        );
+    }
+
+    #[test]
+    fn layer_source_display() {
+        assert_eq!(LayerSource::Global.to_string(), "global (mcp.json)");
+        assert_eq!(LayerSource::AppConfig.to_string(), "config (config.yaml)");
+        assert_eq!(LayerSource::Role("dev".into()).to_string(), "role (dev)");
+        assert_eq!(
+            LayerSource::Agent("worker".into()).to_string(),
+            "agent (worker)"
+        );
+        assert_eq!(LayerSource::Session.to_string(), "session (.set)");
+        assert_eq!(
+            LayerSource::Skill("review".into()).to_string(),
+            "skill (review)"
+        );
+        assert_eq!(LayerSource::Node("n1".into()).to_string(), "node (n1)");
+    }
+}
diff --git a/src/config/mod.rs b/src/config/mod.rs
index e89caee..4832c9e 100644
--- a/src/config/mod.rs
+++ b/src/config/mod.rs
@@ -8,6 +8,7 @@ pub(crate) mod instructions;
 mod macro_policy;
 mod macros;
 mod mcp_factory;
+mod mcp_tool_policy;
 pub(crate) mod memory;
 pub(crate) mod paths;
 pub(crate) mod prompts;
diff --git a/src/config/request_context.rs b/src/config/request_context.rs
index b8a7368..94092c8 100644
--- a/src/config/request_context.rs
+++ b/src/config/request_context.rs
@@ -5599,6 +5599,7 @@ mod tests {
                         url: None,
                         headers: None,
                         oauth: None,
+                        allowed_tools: None,
                     },
                 );
             }
diff --git a/src/mcp/manage.rs b/src/mcp/manage.rs
index c9d4a53..aae7598 100644
--- a/src/mcp/manage.rs
+++ b/src/mcp/manage.rs
@@ -242,6 +242,7 @@ fn build_stdio(cli: &Cli, has_url: bool) -> Result<McpServer> {
         url: None,
         headers: None,
         oauth: None,
+        allowed_tools: None,
     })
 }
 
@@ -300,6 +301,7 @@ fn build_remote(cli: &Cli, transport: McpTransportType, has_command: bool) -> Re
         url: Some(url),
         headers: (!headers.is_empty()).then_some(headers),
         oauth,
+        allowed_tools: None,
     })
 }
 
diff --git a/src/mcp/mod.rs b/src/mcp/mod.rs
index 99d8272..72f3930 100644
--- a/src/mcp/mod.rs
+++ b/src/mcp/mod.rs
@@ -6,7 +6,7 @@ mod sse_transport;
 
 use crate::config::AppConfig;
 use crate::config::paths;
-use crate::utils::{AbortSignal, abortable_run_with_spinner};
+use crate::utils::{AbortSignal, abortable_run_with_spinner, dimmed_text};
 use crate::vault::Vault;
 use crate::vault::interpolate_secrets;
 use anyhow::Error;
@@ -166,6 +166,8 @@ pub(crate) struct McpServer {
     pub headers: Option<IndexMap<String, String>>,
     #[serde(skip_serializing_if = "Option::is_none")]
     pub oauth: Option<McpOAuthConfig>,
+    #[serde(rename = "allowedTools", skip_serializing_if = "Option::is_none")]
+    pub allowed_tools: Option<Vec<String>>,
 }
 
 impl McpServer {
@@ -177,6 +179,15 @@ impl McpServer {
     }
 
     pub fn validate(&self, name: &str) -> Result<()> {
+        if let Some(tools) = &self.allowed_tools
+            && tools.is_empty()
+        {
+            let message = format!(
+                "MCP server '{name}' has an empty \"allowedTools\" list, so none of its tools will be callable"
+            );
+            warn!("{message}");
+            eprintln!("{}", dimmed_text(&message));
+        }
         if self.is_remote() {
             let type_label = match self.transport_type {
                 McpTransportType::Http => "http",
@@ -802,6 +813,7 @@ mod tests {
             url: None,
             headers: None,
             oauth: None,
+            allowed_tools: None,
         }
     }
 
@@ -815,6 +827,7 @@ mod tests {
             url: Some(url.to_string()),
             headers: None,
             oauth: None,
+            allowed_tools: None,
         }
     }
 
@@ -828,6 +841,7 @@ mod tests {
             url: Some(url.to_string()),
             headers: None,
             oauth: None,
+            allowed_tools: None,
         }
     }
 
@@ -860,6 +874,7 @@ mod tests {
             url: None,
             headers: None,
             oauth: None,
+            allowed_tools: None,
         };
 
         let err = spec.validate("test").unwrap_err();
@@ -878,6 +893,7 @@ mod tests {
             url: Some("http://localhost".into()),
             headers: None,
             oauth: None,
+            allowed_tools: None,
         };
 
         let err = spec.validate("test").unwrap_err();
@@ -898,6 +914,7 @@ mod tests {
             url: None,
             headers: Some(headers),
             oauth: None,
+            allowed_tools: None,
         };
 
         let err = spec.validate("test").unwrap_err();
@@ -923,6 +940,7 @@ mod tests {
             url: None,
             headers: None,
             oauth: None,
+            allowed_tools: None,
         };
 
         let err = spec.validate("test").unwrap_err();
@@ -941,6 +959,7 @@ mod tests {
             url: Some("http://localhost".into()),
             headers: None,
             oauth: None,
+            allowed_tools: None,
         };
 
         let err = spec.validate("test").unwrap_err();
@@ -959,6 +978,7 @@ mod tests {
             url: Some("http://localhost".into()),
             headers: None,
             oauth: None,
+            allowed_tools: None,
         };
 
         let err = spec.validate("test").unwrap_err();
@@ -977,6 +997,7 @@ mod tests {
             url: Some("http://localhost".into()),
             headers: None,
             oauth: None,
+            allowed_tools: None,
         };
 
         let err = spec.validate("test").unwrap_err();
@@ -1002,6 +1023,7 @@ mod tests {
             url: None,
             headers: None,
             oauth: None,
+            allowed_tools: None,
         };
 
         let err = spec.validate("test").unwrap_err();