Implemented selective disable of tools to spare with the initial schema size (#1035)

* feat(mcp): selectively disable tools to reduce initial schema size

* fix(mcp): address greptile review feedback

- Reorder createCallToolHandler so the disabled-tool check runs before
  validateMultiRepoAccess, giving config-disabled tools a consistent
  "Unknown tool" response regardless of multi-repo state.
- Mark CodegraphConfig.mcp.disabledTools optional to match the runtime
  guard (config.mcp?.disabledTools) and tolerate partial configs.
- Update list_repos single-repo test to reflect the unified
  "Unknown tool" path.
- Apply biome formatting to normalizeToolName.

* docs(mcp): document mcp.disabledTools config

- README: short subsection under Configuration with example and link.
- docs/guides/mcp-tool-filtering.md: extensive guide covering motivation,
  name normalization, runtime behavior, full tool catalog, and recipes.

* docs(config): replace mcp-only guide with full config reference

Per review feedback, the previous guide was too narrowly scoped. Replace
with docs/guides/configuration.md covering every key in DEFAULTS:
file selection, build, query, embeddings, llm, search, ci, manifesto,
check, coChange, analysis, community, structure, risk, display, mcp.

README points to the new guide and keeps the short MCP tool-filtering
example for the PR's headline feature.

* fix(mcp): simplify disabledTools to always be an array (#1035)

Impact: 1 functions changed, 1 affected

* refactor(mcp): remove unreachable list_repos branch (#1035)

The 'list_repos' tool is excluded from 'enabledToolNames' when 'multiRepo'
is false, so 'createCallToolHandler' rejects single-repo 'list_repos'
calls with 'Unknown tool' before they ever reach 'validateMultiRepoAccess'.
That made the 'name === "list_repos"' branch unreachable. Drop the dead
branch and the now-unused 'name' parameter; existing test
'rejects list_repos in single-repo mode' covers the early-rejection path.

---------

Co-authored-by: carlos-alm <contato@carlosalmeida.com>
Co-authored-by: carlos-alm <127798846+carlos-alm@users.noreply.github.com>

Author: kecsap

README.md

@@ -773,7 +773,7 @@ Copy `.github/workflows/codegraph-impact.yml` to your repo, and every PR will ge
 
 ## 🛠️ Configuration
 
-Create a `.codegraphrc.json` in your project root to customize behavior:
+Create a `.codegraphrc.json` in your project root to customize behavior. The snippets below cover the most-used keys — see **[docs/guides/configuration.md](docs/guides/configuration.md)** for the full reference (every group, every key, every default).
 
 ```json
 {
@@ -833,6 +833,20 @@ The command is split on whitespace and executed with `execFileSync` (no shell in
 
 Works with any secret manager: 1Password CLI (`op`), Bitwarden (`bw`), `pass`, HashiCorp Vault, macOS Keychain (`security`), AWS Secrets Manager, etc.
 
+### MCP tool filtering
+
+Codegraph's MCP server exposes 30+ tools by default. For models with a small context window, you can shrink the schema by disabling tools you don't use:
+
+```json
+{
+  "mcp": {
+    "disabledTools": ["execution_flow", "sequence", "communities", "co_changes"]
+  }
+}
+```
+
+Names are matched case-insensitively and a leading `codegraph<digits>_` prefix (e.g. `codegraph2_module_map`) is stripped before comparison. Disabled tools are removed from `tools/list` and any `tools/call` invocation returns `Unknown tool: <name>`. See **[docs/guides/configuration.md#mcp-tool-filtering](docs/guides/configuration.md#mcp-tool-filtering)** for the full tool catalog, and the rest of that guide for every other config option.
+
 ## 📖 Programmatic API
 
 Codegraph also exports a full API for use in your own tools: