feat: expose all 10 MCP tools via CLI + document them (#42)

* test: decision card output shape and scope-prefixed snippets

* docs: release notes for ranked search and edit decision card

* sanitize docs, one last moment fix

* feat: expose all 10 MCP tools via CLI + document them

- Add handleCliCommand() in src/cli.ts with 8 new subcommands:
  search, metadata, status, reindex, style-guide, patterns, refs, cycles
- Each maps 1:1 to existing tool handlers via dispatchTool()
- Create initToolContext() that builds ToolContext from persisted index
- Add required-flag validation (--query for search, --symbol for refs)
- Support --json flag for scripting/piping
- Update src/index.ts routing to send CLI_SUBCOMMANDS to handleCliCommand
- Expand README "CLI Access" → "CLI Reference" with all 9 commands
- Add "CLI Reference" section to docs/capabilities.md with command table

CLI now enables vendor-neutral access for scripting, debugging, and CI.

Co-Authored-By: Claude Haiku 4.5 <noreply@anthropic.com>

* refactor: clean up imports and improve error handling

- Removed unused import of Memory from src/index.ts.
- Simplified error message construction in src/core/symbol-references.ts.
- Reorganized risk level calculation in src/tools/search-codebase.ts for clarity and consistency.
- Added a TODO comment for reviewing confidence calculation in src/tools/search-codebase.ts.

* refactor: update risk level calculation in search-codebase.ts

- Renamed riskLevel variable to _riskLevel for clarity.
- Added a TODO comment to review the risk level calculation logic.
- Adjusted risk level assignment based on cycle count and impact candidates.

* refactor: clean up CLI command output and improve error message formatting

- Consolidated console.log statements in src/cli.ts for better readability.
- Enhanced error message formatting in src/core/symbol-references.ts and src/tools/search-codebase.ts for consistency.
- Streamlined conditional object construction in src/tools/search-codebase.ts for clarity.

---------

Co-authored-by: Claude Haiku 4.5 <noreply@anthropic.com>

Author: PatrickSys

README.md

@@ -287,31 +287,52 @@ Structured filters available: `framework`, `language`, `componentType`, `layer`
 !.codebase-context/memory.json
 ```
 
-## CLI Access (Vendor-Neutral)
+## CLI Reference
 
-You can manage team memory directly from the terminal without any AI agent:
+All MCP tools are available as CLI commands — no AI agent required. Useful for scripting, debugging, and CI workflows.
+
+Set `CODEBASE_ROOT` to your project root, or run from the project directory.
 
 ```bash
-# List all memories
-npx codebase-context memory list
+# Search the indexed codebase
+npx codebase-context search --query "authentication middleware"
+npx codebase-context search --query "auth" --intent edit --limit 5
 
-# Filter by category or type
-npx codebase-context memory list --category conventions --type convention
+# Project structure, frameworks, and dependencies
+npx codebase-context metadata
 
-# Search memories
-npx codebase-context memory list --query "auth"
+# Index state and progress
+npx codebase-context status
 
-# Add a memory
-npx codebase-context memory add --type convention --category tooling --memory "Use pnpm, not npm" --reason "Workspace support and speed"
+# Re-index the codebase
+npx codebase-context reindex
+npx codebase-context reindex --incremental --reason "added new service"
 
-# Remove a memory
-npx codebase-context memory remove <id>
+# Style guide rules
+npx codebase-context style-guide
+npx codebase-context style-guide --query "naming" --category patterns
+
+# Team patterns (DI, state, testing, etc.)
+npx codebase-context patterns
+npx codebase-context patterns --category testing
 
-# JSON output for scripting
-npx codebase-context memory list --json
+# Symbol references
+npx codebase-context refs --symbol "UserService"
+npx codebase-context refs --symbol "handleLogin" --limit 20
+
+# Circular dependency detection
+npx codebase-context cycles
+npx codebase-context cycles --scope src/features
+
+# Memory management
+npx codebase-context memory list
+npx codebase-context memory list --category conventions --type convention
+npx codebase-context memory list --query "auth" --json
+npx codebase-context memory add --type convention --category tooling --memory "Use pnpm, not npm" --reason "Workspace support and speed"
+npx codebase-context memory remove <id>
 ```
 
-Set `CODEBASE_ROOT` to point to your project, or run from the project directory.
+All commands accept `--json` for raw JSON output suitable for piping and scripting.
 
 ## Tip: Ensuring your AI Agent recalls memory:
 

docs/capabilities.md

@@ -2,6 +2,35 @@
 
 Technical reference for what `codebase-context` ships today. For the user-facing overview, see [README.md](../README.md).
 
+## CLI Reference
+
+All 10 MCP tools are exposed as CLI subcommands. Set `CODEBASE_ROOT` or run from the project directory.
+
+| Command | Flags | Maps to |
+|---|---|---|
+| `search --query <q>` | `--intent explore\|edit\|refactor\|migrate`, `--limit <n>`, `--lang <l>`, `--framework <f>`, `--layer <l>` | `search_codebase` |
+| `metadata` | — | `get_codebase_metadata` |
+| `status` | — | `get_indexing_status` |
+| `reindex` | `--incremental`, `--reason <r>` | `refresh_index` |
+| `style-guide` | `--query <q>`, `--category <c>` | `get_style_guide` |
+| `patterns` | `--category all\|di\|state\|testing\|libraries` | `get_team_patterns` |
+| `refs --symbol <name>` | `--limit <n>` | `get_symbol_references` |
+| `cycles` | `--scope <path>` | `detect_circular_dependencies` |
+| `memory list` | `--category`, `--type`, `--query`, `--json` | — |
+| `memory add` | `--type`, `--category`, `--memory`, `--reason` | `remember` |
+| `memory remove <id>` | — | — |
+
+All commands accept `--json` for raw JSON output. Errors go to stderr with exit code 1.
+
+```bash
+# Quick examples
+npx codebase-context status
+npx codebase-context search --query "auth middleware" --intent edit
+npx codebase-context refs --symbol "UserService" --limit 10
+npx codebase-context cycles --scope src/features
+npx codebase-context reindex --incremental
+```
+
 ## Tool Surface
 
 10 MCP tools + 1 optional resource (`codebase://context`). **Migration:** `get_component_usage` was removed; use `get_symbol_references` for symbol usage evidence.

package.json

@@ -128,7 +128,7 @@
     "@typescript-eslint/typescript-estree": "^7.0.0",
     "fuse.js": "^7.0.0",
     "glob": "^10.3.10",
-    "hono": "4.11.7",
+    "hono": "^4.11.10",
     "ignore": "^5.3.1",
     "typescript": "^5.3.3",
     "uuid": "^9.0.1",
@@ -142,7 +142,7 @@
     "@types/uuid": "^9.0.8",
     "@typescript-eslint/eslint-plugin": "^8.51.0",
     "@typescript-eslint/parser": "^8.51.0",
-    "eslint": "^10.0.1",
+    "eslint": "^9.0.0",
     "eslint-config-prettier": "^10.1.8",
     "eslint-plugin-import": "^2.32.0",
     "globals": "^17.0.0",
@@ -160,7 +160,8 @@
       "sharp"
     ],
     "overrides": {
-      "@modelcontextprotocol/sdk>ajv": "8.18.0"
+      "@modelcontextprotocol/sdk>ajv": "8.18.0",
+      "minimatch": ">=10.2.1"
     }
   }
 }