feat: Complete MCP Implementation with 70+ Tools, Agent Skills & Workflow Improvements

[rishitank]

Summary

This PR implements the complete MCP specification (2025-11-25), adds 70+ tools across multiple categories, introduces an Agent Skills framework for progressive disclosure, and improves development workflows.

MCP Spec Features

Resources Support

• resources/list - List all indexed files as browsable resources
• resources/read - Read file content by URI (file:// scheme) with percent-decoding
• resources/subscribe / resources/unsubscribe - Subscribe to file changes
• Security: Canonical workspace path validation to prevent path traversal

Progress Notifications

• notifications/progress support for long-running operations
• ProgressManager and ProgressReporter for tracking indexing progress
• Token-based progress tracking

Completions API

• completion/complete handler for autocomplete
• File path completions from indexed files and client roots
• Prompt name completions

Request Cancellation

• Track active requests with HashSet<RequestId>
• Separate cancelled_requests set for explicit cancellation tracking
• Handle notifications/cancelled to cancel in-progress operations

Roots Support

• Parse client workspace roots from initialize params
• Store roots for file path resolution and completions

Prompt Templates

• prompts/list and prompts/get handlers
• Built-in prompts: code_review, explain_code, write_tests
• PromptRegistry with proper conditional template handling (mid-line {{#if}} blocks)

Logging Support

• logging/setLevel handler per MCP spec
• RFC 5424 severity levels (Debug, Info, Notice, Warning, Error, Critical, Alert, Emergency)

Tool Annotations (MCP Spec 2025-11-25)

• readOnlyHint, destructiveHint, idempotentHint, openWorldHint
• Human-readable title for all tools

Tools (70+)

Navigation Tools (3)

Tool	Description
find_references	Find all usages of a symbol in the codebase
go_to_definition	Find where a symbol is defined
diff_files	Compare two files with unified diff output

Workspace Tools (7)

Tool	Description
workspace_stats	Get file counts, lines of code, language breakdown
git_status	Get staged, unstaged, untracked files with optional diff
extract_symbols	Extract functions, classes, structs from source files
git_log	Get commit history with filtering options
git_diff	Get diff between commits/branches
dependency_graph	Analyze import/dependency relationships
file_history	Get git history for a specific file

Specialized Search Tools (7)

Tool	Description
search_tests_for	Find test files related to a query
search_config_for	Find configuration files related to a query
search_callers_for	Find callers/usages of a symbol
search_importers_for	Find files importing a module/symbol
info_request	Simplified codebase retrieval with explanation mode
pattern_search	Structural code pattern matching
context_search	Context-aware semantic search

Memory Tools (4)

Tool	Description
memory_store	Store key-value pairs persistently
memory_retrieve	Retrieve stored values
memory_list	List all stored keys
memory_delete	Delete stored values

Skills Tools (2)

Tool	Description
search_skills	Search available agent skills by keyword
load_skill	Load a skill's SKILL.md content

Core Tools (47+)

• File operations, search, retrieval, code analysis, and more

Agent Skills Framework

Implements Anthropic's Agent Skills architecture for progressive disclosure:

Built-in Skills (7)

Skill	Description
planning	Task decomposition and project planning
code_review	Code quality analysis and review
search_patterns	Effective codebase search strategies
debugging	Systematic debugging workflows
refactoring	Safe code refactoring techniques
documentation	Documentation generation and maintenance
testing	Test writing and coverage strategies

Skills as MCP Prompts

All skills are exposed via prompts/list and prompts/get for AI client integration.

Multi-Language Symbol Detection

Supports symbol extraction for:

• Rust: fn, struct, enum, trait, impl
• Python: def, class, async def
• TypeScript/JavaScript: function, class, interface, type
• Go: func, type struct, type interface

Security Fixes

• Path traversal protection in DependencyGraphTool and complete_file_path
• Canonical workspace path validation in resource reading
• Template literal injection prevention in GitHub Actions workflows
• Regex escaping for user input with regex::escape()
• Proper error propagation for invalid regex patterns

Workflow Improvements

Release Workflow

• Triggers automatically after successful CI on main branch
• Automatic version bumping with patch/minor/major options
• AI-powered changelog generation
• Duplicate tag protection

Dependabot

• Configured for Cargo, GitHub Actions, and Docker
• Weekly updates with grouped PRs

SDK Sync Workflow

• Weekly health check for SDK compatibility
• Creates tracking issues for review
• Template literal injection prevention

CI Improvements

• MSRV declared: rust-version = "1.82" in Cargo.toml
• Clippy with -D warnings flag

Testing

• ✅ 244 unit tests pass
• ✅ Integration tests for MCP protocol
• ✅ Clippy passes with no warnings
• ✅ Cargo fmt applied

Test Coverage

• Resources: MIME types, serialization, security
• Progress: ProgressReporter, ProgressManager, ProgressToken
• Navigation: Pattern matching, language detection, diff generation
• Workspace: Symbol detection for Rust/Python/TypeScript/Go
• Skills: Loading, searching, frontmatter parsing
• Memory: Store, retrieve, list, delete operations
• Prompts: Template substitution, conditional handling

Code Review Fixes

All CodeRabbit review comments addressed:

Issue	Commit	Fix
Template literal injection	b1518b5	Environment variable approach
Template substitution	b1518b5	Proper mid-line conditional handling
File URI construction	b1518b5	Backslash normalization
Security check	b1518b5	Canonical workspace path
Cancellation logic	b1518b5	Separate cancelled_requests set
Percent-decoding	07e9094-7e65250	percent_decode_str for URIs
load_skill error handling	aa64cef	Uses error_result helper
parse_frontmatter bounds	aa64cef	Safe string slicing
MSRV declaration	1cde7d5	rust-version = "1.82"
Hardcoded repo paths	1cde7d5	{owner}/{repo} placeholders
Regex escaping	1cde7d5	regex::escape() for user input
Regex pre-compilation	1cde7d5	Vec<Regex> before loops
Clippy warning	776dbd8	assert! instead of assert_eq!
include_related flag	e38ce36	Reduces max_tokens when false
Regex error propagation	a64e759	Returns Result with proper errors

Files Changed

• 45 files changed
• 15,915 additions
• 143 deletions
• 39 commits

Next Steps After Merge

1. Set up branch protection for main
2. Bump version in Cargo.toml to trigger release
3. Consider adding more skills based on usage patterns