feat(mcp): pare default tool surface to codegraph_explore alone + redux-thunk synthesizer

src/installer/instructions-template.ts

@@ -17,8 +17,8 @@
  *    runs without this block, and consistently with it — including runs
  *    with zero Read/grep fallback.
  *  - **Non-MCP harnesses** — agents with no MCP client at all can still
- *    run the `codegraph explore` / `codegraph node` CLI, which prints the
- *    same output as the MCP tools.
+ *    run the `codegraph explore` CLI, which prints the same output as the
+ *    MCP tool.
  *
  * Keep this block SHORT. The main agent reads it every turn on top of the
  * server instructions — the #529 duplication-cost argument still bounds
@@ -44,8 +44,8 @@ export const CODEGRAPH_INSTRUCTIONS_BLOCK = `${CODEGRAPH_SECTION_START}
 
 In repositories indexed by CodeGraph (a \`.codegraph/\` directory exists at the repo root), reach for it BEFORE grep/find or reading files when you need to understand or locate code:
 
-- **MCP tools** (when available): \`codegraph_explore\` answers most code questions in one call — the relevant symbols' verbatim source plus the call paths between them. \`codegraph_node\` returns one symbol's source + callers, or reads a whole file with line numbers. If the tools are listed but deferred, load them by name via tool search.
-- **Shell** (always works): \`codegraph explore "<symbol names or question>"\` and \`codegraph node <symbol-or-file>\` print the same output.
+- **MCP tool** (when available): \`codegraph_explore\` answers most code questions in one call — the relevant symbols' verbatim source plus the call paths between them, including dynamic-dispatch hops grep can't follow. Name a file or symbol in the query to read its current line-numbered source. If it's listed but deferred, load it by name via tool search.
+- **Shell** (always works): \`codegraph explore "<symbol names or question>"\` prints the same output.
 
 If there is no \`.codegraph/\` directory, skip CodeGraph entirely — indexing is the user's decision.
 ${CODEGRAPH_SECTION_END}`;

src/installer/targets/shared.ts

@@ -31,20 +31,21 @@ export function getMcpServerConfig(): { type: string; command: string; args: str
 
 /**
  * Permissions list for Claude `settings.json`. Other targets that
- * have a permissions concept can compose this list directly. The
- * permission strings follow Claude's `mcp__<server>__<tool>` format.
+ * have a permissions concept can compose this list directly.
+ *
+ * One server-scoped wildcard rather than a per-tool list. By default only
+ * `codegraph_explore` is even LISTED to the agent (see DEFAULT_MCP_TOOLS in
+ * mcp/tools.ts), so in practice explore is the only tool this auto-approves —
+ * but the wildcard means that if a user re-enables another tool via
+ * CODEGRAPH_MCP_TOOLS, it's already pre-approved (no permission prompt, no
+ * hand-editing settings.json), and future tools are covered too. Claude only
+ * honors globs after a literal `mcp__<server>__` prefix, so this exact string
+ * is the way to allow-all for one server; a bare `mcp__codegraph` or `*` is
+ * ignored. The allowlist gates PROMPTING, not visibility, so a superset here
+ * never makes a hidden tool appear.
  */
 export function getCodeGraphPermissions(): string[] {
-  return [
-    'mcp__codegraph__codegraph_explore',
-    'mcp__codegraph__codegraph_search',
-    'mcp__codegraph__codegraph_node',
-    'mcp__codegraph__codegraph_callers',
-    'mcp__codegraph__codegraph_callees',
-    'mcp__codegraph__codegraph_impact',
-    'mcp__codegraph__codegraph_files',
-    'mcp__codegraph__codegraph_status',
-  ];
+  return ['mcp__codegraph__*'];
 }
 
 /**