MCP server CodeSift

CodeSift -- Token-efficient code intelligence for AI agents

CodeSift indexes your codebase with tree-sitter AST parsing and gives AI agents 150 MCP tools (55 core + 95 discoverable) via CLI or MCP server. It uses 61-95% fewer tokens than raw grep/Read workflows on typical code navigation tasks.

Works with: Claude Code, Cursor, Codex, Gemini CLI, Zed, Aider, Continue — any MCP client.

Install

Bulletproof one-liner (clears stale cache, installs latest, auto-configures all platforms):

npm cache clean --force && npm i -g codesift-mcp@latest

npm cache clean --force clears stale registry metadata that can cause ETARGET errors. The postinstall script then runs codesift setup all automatically.

Restart your AI client (close + reopen) so the new MCP server is picked up. New terminal sessions in your IDE work fine — no need to quit the IDE itself.

Windows: close every MCP client before upgrading (Claude Code, Codex, Cursor, …). A running CodeSift server holds native .node files open (onnxruntime-node, @huggingface/transformers), Windows will not let npm replace an open file, and the upgrade fails with EBUSY / EPERM.

To configure individual platforms manually:

codesift setup claude    # Claude Code — config + rules + hooks + CLAUDE.md
codesift setup codex     # Codex CLI — config + AGENTS.md rules
codesift setup cursor    # Cursor IDE — config + .cursor/rules
codesift setup gemini    # Gemini CLI — config + GEMINI.md rules
codesift setup antigravity # Google Antigravity — config only
codesift setup all       # All platforms at once

Verify installed version:

codesift --version

What setup installs (all by default):

Component	What it does	Opt-out
MCP config	Registers codesift-mcp server	(required)
Rules file	Tool mapping, hints, ALWAYS/NEVER rules for your AI agent	--no-rules
Hooks (where supported)	Auto-index after Edit/Write, redirect large Read/Bash flows to CodeSift	--no-hooks

Additionally, every MCP client receives ~800 tokens of compact guidance automatically via the MCP instructions field — zero setup needed.

Update

npm update -g codesift-mcp
codesift setup all              # Updates rules files to latest version
codesift setup all --force      # Force-update even if you modified rules

setup writes the absolute codesift-mcp bin path when available. This avoids per-session npx cache drift and stale dist/server.js paths. Re-run setup after updating to refresh rules files and repair old MCP config entries.

Quick start

# Index a project
codesift index /path/to/project

# Search for a function
codesift symbols local/my-project "createUser" --kind function --include-source

# Semantic search (requires embedding provider)
codesift retrieve local/my-project \
  --queries '[{"type":"semantic","query":"how does caching work?"}]'

# Build the project wiki — agents read it on every new session
codesift wiki-generate

Wiki tip: setup --hooks (on by default) wires a SessionStart hook that injects a project overview into every new agent session, plus a PostToolUse hook that auto-refreshes it. Both are silent no-ops until you run codesift wiki-generate once in the repo — skip it and the wiki never reaches your agent. This is the #1 reason wiki adoption stays at zero.

Benchmark results

Combo benchmark (real-world tool sequences)

772 real tasks from usage.jsonl — exact query sequences agents used across 33+ repos. Native (grep/find/read) vs CodeSift.

Sequence	Runs	Tok native	Tok Sift	Delta	Wins
pat→st→pat→st (4-gram)	37	377,258	36,758	-90%	28/37
pat→st→pat	39	186,436	20,500	-89%	31/39
st→pat→st→pat	35	307,490	35,905	-88%	25/35
ss→st	78	202,837	36,408	-82%	35/78
st→pat→st	40	250,240	44,424	-82%	27/40
st→tree→st	28	262,703	61,093	-77%	22/28
tree→st	57	380,324	133,578	-65%	44/57
AGGREGATE	772	5,130,240	1,994,825	-61%	542/772

Per-tool (single-tool benchmark)

Tool	Tok native	Tok Sift	Delta
search_text vs rg	1,015,245	49,718	-95%
search_symbols vs rg	192,486	34,186	-82%
get_file_outline vs Read	91,796	58,229	-37%

Performance features

Feature	Description	Impact
mtime-based incremental indexing	Skip files with unchanged mtime on reindex	5.6x faster reindex (57s → 10s on 778-file repo)
index_file	Re-index a single file without full repo walk	9ms when the file is unchanged (short-circuit); a changed file costs one row write, not a whole-index rewrite
SQLite index	Normalized per-repo DB in WAL mode; incremental writes touch one file's rows (details)	10.8x faster single-file re-index, ~17800x faster warm index load
detail_level on search_symbols	compact (~15 tok/result), standard, full	compact is 63% fewer tokens than standard
token_budget on search_symbols	Pack results to token limit instead of guessing top_k	Precise budget control
Centrality bonus in BM25	Symbols in frequently-imported files rank higher	Core utilities surface first in search
Response dedup cache	Identical calls within 30s return cached result	Eliminates duplicate API calls
In-flight dedup	Parallel identical requests coalesce into one	Prevents race condition duplicates
Auto-grouping	Force group_by_file when output exceeds 80K chars	Prevents 100K+ token responses
Relevance-gap filtering	Cut search results below 15% of top score	50→21 results (cleaner output)
Semantic chunking	Chunk by symbol boundaries, not fixed lines	Functions stay intact for semantic search
Token savings display	"Saved ~X tokens ($Y)" on every response	Visible ROI per call
Framework-aware dead code	Whitelist React hooks, NestJS lifecycle, Next.js handlers	<10% false positives (was ~40%)
Mermaid diagrams	detect_communities, get_knowledge_map, trace_route output Mermaid	Paste-ready architecture diagrams
HTML report	generate_report → standalone browser report	Complexity, dead code, hotspots, communities
Progressive cascade	>15K tok → compact format, >25K → counts only, >30K → truncate	Auto-adjusting response size
Tool visibility	Non-core tools hidden via MCP disable(), discoverable on demand	~10K fewer tokens in system prompt
MCP instructions	~800 tok of agent guidance sent automatically to every client	Zero-setup onboarding
Ranked search	search_text(ranked=true) classifies hits by containing symbol, deduplicates	Saves 1-3 follow-up calls
PreToolUse hooks	Redirect large-file Read to CodeSift outline/search	Prevents 5K+ token file dumps
PostToolUse hooks	Auto-reindex after Edit/Write	Always-fresh index
Sequential hints	Prepended hints (H1-H9) suggest batching after 3+ consecutive calls	Guides agents toward efficient usage
Wiki generation	generate_wiki produces markdown wiki from code topology	Architecture docs from Louvain communities + hubs + surprises
Lens HTML	Self-contained HTML dashboard with D3 chord diagram	Visual architecture overview in one file
Wiki hook inject	PreToolUse injects community context on file Read	Agent gets architectural context automatically

CLI commands

Indexing

Command	Description
codesift index <path>	Index a local folder (mtime-based incremental — skips unchanged files)
codesift index-repo <url>	Clone and index a remote git repository
codesift repos	List all indexed repositories
codesift invalidate <repo>	Clear index cache for a repository

Search

Command	Description
codesift search <repo> <query>	Full-text search across all files
codesift symbols <repo> <query>	Search symbols by name/signature (supports --detail compact|standard|full and --token-budget N)

Outline

Command	Description
codesift tree <repo>	File tree with symbol counts
codesift outline <repo> <file>	Symbol outline of a single file
codesift repo-outline <repo>	High-level repository outline

Symbol retrieval

Command	Description
codesift symbol <repo> <id>	Get a single symbol by ID
codesift symbols-batch <repo> <ids...>	Get multiple symbols by ID
codesift find <repo> <query>	Find symbol and show source
codesift refs <repo> <name>	Find all references to a symbol
codesift context-bundle <repo> <name>	Symbol + imports + siblings + types used in one call

Graph & analysis

Command	Description
codesift trace <repo> <name>	Trace call chain (callers/callees). Supports --format mermaid for flowchart output.
codesift impact <repo> --since <ref>	Blast radius of git changes + affected tests + risk scores per file
codesift context <repo> <query>	Assemble relevant code context. Supports --level L0|L1|L2|L3 for compression.
codesift knowledge-map <repo>	Module dependency map with circular dependency detection
codesift trace-route <repo> <path>	Trace HTTP route → handler → service → DB calls (NestJS/Next.js/Express/Ktor/Spring Boot Kotlin)
codesift communities <repo>	Louvain community detection — discover code clusters from import graph

Code analysis

Command	Description
codesift dead-code <repo>	Find exported symbols with zero external references
codesift complexity <repo>	Cyclomatic complexity + nesting depth per function
codesift clones <repo>	Copy-paste detection (hash bucketing + line similarity)
codesift dup-check [--base <ref>]	Gate for new code: is anything added since merge-base <base> HEAD (incl. uncommitted and untracked files) a copy of existing code? Exit 1 on findings — for pre-push hooks and reviews. Suppress with // codesift-dup-ok: <reason>
codesift hotspots <repo>	Git churn x complexity = risk-ranked file list
codesift patterns <repo> <pattern>	Structural anti-pattern search (33 built-in + custom regex)

Wiki & Lens

Command	Description
codesift wiki-generate	Generate wiki pages + Lens HTML from code topology (communities, hubs, surprises, hotspots)
codesift wiki-generate --focus src/tools	Scope wiki to a specific directory
codesift wiki-generate --no-lens	Skip Lens HTML generation
codesift wiki-lint <wiki-dir>	Check wiki for broken links, orphan pages, stale content

Output goes to .codesift/wiki/ in the repo root. Includes markdown pages with [[wikilinks]], backlinks, community summaries, and a self-contained codesift-lens.html with D3 chord diagram and force-directed graph.

Cross-repo

Command	Description
codesift cross-search <query>	Search symbols across ALL indexed repositories
codesift cross-refs <name>	Find references across ALL indexed repositories

Diff

Command	Description
codesift diff <repo> --since <ref>	Structural diff between git refs
codesift changed <repo> --since <ref>	List changed symbols between refs

Batch & utility

Command	Description
codesift retrieve <repo> --queries <json>	Batch multiple queries in one call
codesift stats	Show usage statistics
codesift generate-claude-md <repo>	Generate CLAUDE.md project summary
codesift list-patterns	List all built-in anti-pattern names

MCP tools (146 total — 55 core + 95 discoverable)

When running as an MCP server, CodeSift exposes 51 core tools directly. The remaining 95 niche tools are discoverable via discover_tools and describe_tools, or via plan_turn which routes a natural-language task to the best-fit tools and auto-reveals any hidden ones.

Category	Tools
Indexing	index_folder (mtime skip, dirty propagation), index_repo, index_file (single-file reindex, 9ms), list_repos, invalidate_cache
Search	search_symbols (detail_level: compact/standard/full, token_budget, kind filter incl. component/hook), search_text (auto_group, group_by_file, ranked)
Outline	get_file_tree, get_file_outline, get_repo_outline, suggest_queries (React-aware: suggests component/hook queries when detected)
Symbol retrieval	get_symbol, get_symbols, find_and_show, get_context_bundle (React enrichment: hooks_used, child_components, parent_components, wrapper pattern)
References & graph	find_references (LSP-enhanced), trace_call_chain (JSX-aware: <Component> = call edge; filter_react_hooks option), impact_analysis, trace_route (HTTP route → handler → DB — NestJS/Next.js/Express/Ktor/Spring Boot/Yii2/Laravel)
React	trace_component_tree (BFS JSX composition tree with Mermaid output), analyze_hooks (hook inventory, Rule of Hooks violations, custom hook composition), analyze_renders (re-render risk: inline props, missing memo, children-aware threshold, markdown output), analyze_context_graph (createContext → Provider → useContext consumer mapping)
LSP bridge	go_to_definition (LSP + index fallback), get_type_info (hover), rename_symbol (cross-file type-safe rename)
Context & knowledge	assemble_context (level: L0/L1/L2/L3), get_knowledge_map, detect_communities (Louvain)
Conversation search	index_conversations, search_conversations, find_conversations_for_symbol
Diff	diff_outline, changed_symbols
Batch retrieval	codebase_retrieval (batch multiple sub-queries with shared token budget, incl. type: "conversation")
Security	scan_secrets (AST-aware secret detection, ~1,100 rules, masked output)
PHP / Yii2	resolve_php_namespace (PSR-4 FQCN→file), trace_php_event (event→listener chain), find_php_views (render→view mapping), resolve_php_service (Yii::$app→concrete class), php_security_scan (compound: SQL injection, XSS, eval, exec, unserialize), php_project_audit (meta-tool — includes ActiveRecord analysis, N+1 detection, god-model detection via checks= parameter)
Analysis	find_dead_code (framework-aware incl. React/Next.js route entry points), analyze_complexity (React: hook_count, state_count, effect_count, jsx_depth), find_clones, analyze_hotspots, search_patterns (33 built-in: JS/TS ×9, React ×20, Kotlin ×6, PHP ×4), list_patterns, frequency_analysis (AST subtree clustering), find_perf_hotspots (6 perf anti-patterns: unbounded queries, sync I/O, N+1 loops, unbounded parallel, missing pagination, expensive recompute), explain_query (Prisma→SQL with EXPLAIN ANALYZE), audit_scan (5-gate composite: dead code + clones + patterns + complexity + hotspots)
Architecture	classify_roles (symbol role classification via call graph), check_boundaries (architecture boundary enforcement), ast_query (structural grep via tree-sitter), fan_in_fan_out (import graph coupling: most-imported, most-dependent, hub files, coupling score 0-100), co_change_analysis (temporal coupling from git history: Jaccard similarity, cluster detection), architecture_summary (one-call composite: stack + communities + coupling + circular deps + LOC + entry points, Mermaid output)
Cross-repo	cross_repo_search, cross_repo_refs
Report	generate_report (standalone HTML with complexity, dead code, hotspots, communities), generate_wiki (markdown wiki pages + Lens HTML from code topology — communities, hubs, surprises, hotspots, framework pages)
Tool discovery	discover_tools (keyword search across hidden tools), describe_tools (full schema on demand, optional reveal)
Discovery	plan_turn(query=...) — route natural-language task description to best-fit tools, symbols, and files; returns ranked recommendations with confidence scores, reveal_required hints, and gap analysis
Meta	index_status (check if repo is indexed: file/symbol counts, language breakdown, text_stub languages), analyze_project (stack + conventions detection), get_extractor_versions (parser language support)
Utility	generate_claude_md (architecture + behavioral guidance), usage_stats (with token savings tracking)

Conversation search

Search past Claude Code conversation history — the decisions, rationale, and debugging sessions that shaped your code.

# Index conversations for current project (auto-detected from cwd)
# Also runs automatically at startup via auto-discovery
index_conversations()

# Index a specific project's conversations
index_conversations(project_path="/Users/me/.claude/projects/-Users-me-DEV-my-project")

# Search past conversations
search_conversations(query="auth middleware bug", limit=5)

# Find conversations that discussed a specific code symbol
find_conversations_for_symbol(symbol_name="processPayment", repo="local/my-project")

# In codebase_retrieval batch queries
codebase_retrieval(repo, queries=[
  {"type": "semantic", "query": "how does auth work"},
  {"type": "conversation", "query": "why we chose Redis over Postgres cache"}
])

Features:

• Auto-discovery at startup (zero config)
• Session-end hook for immediate re-indexing
• Noise filtering: tool_result dumps stripped, tool_use truncated, images → [image]
• Compaction-aware: skips summary injections, indexes last summary as meta-doc
• Cross-reference: link code symbols to the conversations that discussed them

Secret scanning

Detect hardcoded secrets (API keys, JWT tokens, passwords, connection strings) in your indexed codebase. Uses ~1,100 detection rules from TruffleHog via @sanity-labs/secret-scan, with CodeSift's tree-sitter AST for false-positive reduction.

# Scan entire repo for secrets
scan_secrets(repo="local/my-project")

# Filter by severity
scan_secrets(repo="local/my-project", severity="critical")

# Only high-confidence findings, including test files
scan_secrets(repo="local/my-project", min_confidence="high", exclude_tests=false)

# Scope to specific directory
scan_secrets(repo="local/my-project", file_pattern="src/config/**")

Features:

• Eager scanning on file change — results are cached and instant on query
• AST-aware confidence: test files, docs, placeholder variables auto-demoted to low
• Masked output — secrets shown as sk-p***hijk, raw values never in cache or logs
• Inline allowlist — add // codesift:allow-secret to suppress a finding
• Config files indexed — .env, .yaml, .toml, .json, .ini, .properties scanned
• Severity mapping: cloud keys (AWS, GCP) = critical, API keys (OpenAI, GitHub) = high
• Inline warnings in index_file responses when secrets detected

Wiki & Lens — auto-generated architecture documentation

Generate browsable wiki pages and an interactive HTML dashboard from your codebase's topology — zero manual writing.

# Generate wiki for current repo
codesift wiki-generate

# Scope to a directory
codesift wiki-generate --focus src/tools

# Check wiki integrity
codesift wiki-lint .codesift/wiki

What it generates (in .codesift/wiki/):

• Community pages — one per Louvain community (module), with members, cohesion score, cross-boundary edges
• Hubs page — top symbols by fan-in (load-bearing code)
• Surprises page — unexpected cross-community connections (structural + temporal coupling)
• Hotspots page — files ranked by git churn × complexity
• Framework pages — conditional pages for Next.js routes, Hono middleware, Astro islands (when detected)
• Index page — links to all pages with [[wikilinks]] and auto-generated backlinks
• Summaries — compact *.summary.md files (~400 tokens) for AI agent context injection

Lens HTML dashboard (codesift-lens.html):

• Self-contained single HTML file — open in any browser, no server needed
• D3 chord diagram showing cross-community connections
• D3 force-directed graph with community nodes
• 5 tabs: Overview, Communities, Hubs, Surprises, Wiki browser
• Dark/light theme, responsive

AI agent integration:

• Hook inject via handlePrecheckRead — when an agent reads a file, it automatically receives the file's community wiki summary as context
• Configurable token budget (2000 chars default)
• Staleness detection — warns when wiki is outdated vs current index

MCP tool:

generate_wiki(repo, focus?, output_dir?, include_lens?)

PHP / Yii2 support

Full PHP code intelligence with first-on-market Yii2 framework awareness. No other general-purpose MCP tool provides static Yii2 intelligence.

Symbol extraction (tree-sitter-based):

• Namespaces, classes, interfaces, traits, enums (PHP 8.1), functions, methods, properties, constants
• PHPDoc extraction, signature extraction with type hints and return types
• PHPUnit test detection: TestCase subclass = test_suite, test* methods = test_case, setUp/tearDown = test_hook

Yii2 framework awareness:

• Convention routing: trace_route("site/index") resolves to SiteController::actionIndex() (incl. module nesting)
• analyze_project detects Yii2 via composer.json and extracts: controllers, models, modules, widgets, behaviors, components, assets, config files
• 6 PHP-specific tools: namespace resolution (PSR-4), event/listener tracing, view mapping, service locator resolution, security scanning, project audit (meta-tool with ActiveRecord analysis, N+1 detection, god-model detection via checks= parameter)
• Auto-load: PHP tools are automatically enabled when composer.json is detected at CWD — no need to call discover_tools/describe_tools first

Laravel support:

• Route tracing via Route::get('/path', [Controller::class, 'method']) pattern matching
• Convention extraction: controllers, middleware, models, routes, migrations

# Trace a Yii2 route
trace_route(repo, path="site/about")

# Analyze ActiveRecord models (via php_project_audit)
php_project_audit(repo, checks=["activerecord"], model_name="User")

# PHP security scan (8 parallel checks)
php_security_scan(repo)

# Resolve PSR-4 namespace to file
resolve_php_namespace(repo, class_name="App\\Models\\User")

LSP bridge: Intelephense configured for go-to-definition, find-references, type-info, and rename across PHP files.