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

[PatrickSys]

Summary

Implements CLI commands for all 10 MCP tools, enabling vendor-neutral access for scripting, debugging, and CI workflows.

• Add 8 new subcommands: search, metadata, status, reindex, style-guide, patterns, refs, cycles
• Each maps directly to existing tool handlers via dispatchTool()
• Create initToolContext() that builds a ToolContext from the persisted on-disk index (no MCP server needed)
• Support --json flag for JSON output (default: human-readable)
• Validate required flags with stderr + exit code 1

Documentation

• Updated README: "CLI Access" → "CLI Reference" with examples for all 9 commands (memory + 8 new)
• Added "CLI Reference" section to docs/capabilities.md with command/flag/tool mapping table

Test Coverage

• All 234 tests pass
• Build is clean
• Manual verification: --help, status, error cases, memory list

🤖 Generated with Claude Code

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[greptile-apps]

Greptile Summary

Exposes all 10 MCP tools as CLI commands for vendor-neutral scripting and debugging. Creates initToolContext() that builds a ToolContext from on-disk index, routing commands via dispatchTool().

Major changes:

• Added 8 new CLI subcommands (search, metadata, status, reindex, style-guide, patterns, refs, cycles) to src/cli.ts
• Each command maps to existing MCP tool handlers
• Supports --json flag for raw output vs human-readable
• Updated README and docs/capabilities.md with comprehensive examples and reference tables
• Refactored src/index.ts to route all CLI commands through handleCliCommand()

Issues found:

• Filter construction bug in search command (lines 205-207) - multiple filter flags will overwrite each other instead of merging

Confidence Score: 4/5

• Safe to merge after fixing the filter construction bug - the logic error will break multi-filter searches but other functionality is solid
• Score reflects one critical logic bug that breaks search when combining multiple filter flags (lang + framework + layer), but the rest of the implementation is clean with good separation of concerns. Tests pass and architecture is sound.
• src/cli.ts lines 205-207 - fix filter merging logic before merge

Important Files Changed

Filename	Overview
src/cli.ts	Added 8 new CLI commands mapping to MCP tools with initToolContext() and dispatchTool() integration. Found one logic bug in filter construction for search command.
src/index.ts	Updated CLI command routing to use handleCliCommand() instead of handleMemoryCli(), added CLI_SUBCOMMANDS array. Clean refactor with no issues.
README.md	Expanded CLI documentation from memory-only to all 10 MCP tools with examples. Well-structured and clear.
docs/capabilities.md	Added comprehensive CLI reference table mapping commands to MCP tools. Good technical documentation.

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart TD
    Start[CLI Entry: npx codebase-context] --> Parse[handleCliCommand argv]
    Parse --> Memory{command === 'memory'?}
    Memory -->|Yes| MemoryCLI[handleMemoryCli]
    Memory -->|No| Init[initToolContext]
    
    Init --> CheckIndex{index exists?}
    CheckIndex -->|Yes| Ready[indexState: 'ready']
    CheckIndex -->|No| Idle[indexState: 'idle']
    
    Ready --> Route[Route by command]
    Idle --> Route
    
    Route --> Search[search → search_codebase]
    Route --> Metadata[metadata → get_codebase_metadata]
    Route --> Status[status → get_indexing_status]
    Route --> Reindex[reindex → refresh_index]
    Route --> StyleGuide[style-guide → get_style_guide]
    Route --> Patterns[patterns → get_team_patterns]
    Route --> Refs[refs → get_symbol_references]
    Route --> Cycles[cycles → detect_circular_dependencies]
    
    Search --> Dispatch[dispatchTool]
    Metadata --> Dispatch
    Status --> Dispatch
    StyleGuide --> Dispatch
    Patterns --> Dispatch
    Refs --> Dispatch
    Cycles --> Dispatch
    
    Reindex --> PerformIndex[ctx.performIndexing]
    PerformIndex --> Dispatch
    
    Dispatch --> Format{--json flag?}
    Format -->|Yes| JSON[console.log raw JSON]
    Format -->|No| Pretty[console.log formatted]
    
    JSON --> End[Exit]
    Pretty --> End

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_{Last reviewed commit: 9a2d523}

[greptile-apps]

_{4 files reviewed, 1 comment}

_{Edit Code Review Agent Settings | Greptile}

[PatrickSys]

@copilot review

[Copilot]

@PatrickSys I've opened a new pull request, #43, to work on those changes. Once the pull request is ready, I'll request review from you.