CodeScope — Project Truth Engine

CodeScope does not understand code. It verifies code.

It transforms source code into verifiable facts, understandable models, and inspectable evidence — enabling AI to validate claims against reality instead of hallucinating.

Version: v0.2.6 | License: Apache 2.0

---

1. What Is CodeScope?

CodeScope is a Project Truth Engine that answers one question:

"Does the code actually do what you claim?"

Not "what does this code mean", but "does the code actually do what you claim?"

It indexes source code into a structured code graph (call graph + reference graph + module knowledge), then exposes 47 MCP tools that let AI agents locate symbols, trace call paths, verify claims, detect documentation drift, and analyze architecture — all with ~98.9% token savings vs reading raw source files.

Supported Languages (8)

Language	Parser	IR Translator	Verified
Python	✅	✅	✅
Go	✅	✅	✅
C	✅	✅	✅
C++	✅	✅	✅
Rust	✅	✅	✅
JavaScript	✅	✅	✅
TypeScript	✅	✅	✅
Java	✅	✅	✅

Tech Stack

Layer	Technology
Parser	tree-sitter (unified AST IR, 8 languages)
Indexer	C++23 (Clang 17+), SQLite (WAL mode, FTS5)
Server	Rust 2024 Edition, MCP Protocol (JSON-RPC 2.0, stdio transport)
Graph Storage	SQLite (sole graph store, CSR adjacency for sub-ms call-graph queries)
Scheduler	Built-in multi-process parallel indexer (chunk-level work-stealing)
Build	CMake 3.30+ (C++), Cargo (Rust)

---

2. Architecture

graph TB
    subgraph "AI Client"
        Client["Claude Desktop / Cursor / Any MCP Client"]
    end

    subgraph "Rust MCP Server"
        MCP["MCP Protocol (JSON-RPC 2.0)<br/>47 tools / stdio transport"]
        DISPATCH["Tool Dispatch<br/>project_id auto-restore"]
    end

    subgraph "C++ Core Engine"
        PARSER["Parser<br/>tree-sitter → unified IR<br/>8 languages"]
        FACTS["Facts Repository<br/>entity / reference / scope / import"]
        RESOLVER["Resolver Pipeline<br/>Constraint Chain"]
        MODEL["Model Engine<br/>Workflow / Capability<br/>Architecture / Contract"]
        INSPECTOR["Inspector<br/>DeadCodeInspector / verify_integrity"]
    end

    subgraph "SQLite (WAL mode)"
        F_STORE["Facts Store<br/>entity / reference / scope / import"]
        S_STORE["Semantic Store<br/>resolved_reference / relation"]
        M_STORE["Model Store<br/>workflow / capability<br/>architecture / contract"]
        E_STORE["Evidence Store<br/>claim / evidence / finding"]
    end

    Client -->|"MCP stdio"| MCP
    MCP --> DISPATCH
    DISPATCH -->|"FFI"| PARSER
    DISPATCH -->|"FFI"| FACTS
    DISPATCH -->|"FFI"| RESOLVER
    DISPATCH -->|"FFI"| MODEL
    DISPATCH -->|"FFI"| INSPECTOR

    PARSER -->|"writes"| F_STORE
    F_STORE -->|"reads"| RESOLVER
    RESOLVER -->|"writes"| S_STORE
    S_STORE -->|"reads"| MODEL
    MODEL -->|"writes"| M_STORE
    M_STORE -->|"reads"| INSPECTOR
    INSPECTOR -->|"writes"| E_STORE

Loading

Pipeline

Source Code
    |
    v
Parser ------------ entity / reference / scope / import
    |
    v
Resolver ---------- resolved_reference / relation
    |
    v
Model Engine ------ workflow / capability / architecture / contract
    |
    v
Inspector --------- evidence / finding

Query Flow

flowchart LR
    Q["MCP Client<br/>tool call"] --> Q1["Server receives<br/>project_id auto-restore"]
    Q1 --> Q2{"Tool type?"}
    Q2 -->|"index_project"| Q3["Spawn worker subprocess<br/>→ memory isolated<br/>→ exits after done"]
    Q2 -->|"query tools"| Q4["C++ FFI → SQLite query<br/>graph_nodes, graph_edges<br/>search_index, ..."]
    Q2 -->|"get_communities"| Q5["Load full graph<br/>Label Propagation<br/>→ JSON with max_communities limit"]
    Q2 -->|"get_hotspots"| Q6["SQL: COUNT(ge.id) JOIN<br/>graph_edges edge_type=1<br/>ORDER BY caller_count"]
    Q4 --> R["Result JSON<br/>back to MCP Client"]
    Q5 --> R
    Q6 --> R

Loading

Two-Phase Indexing

flowchart LR
    subgraph A["Phase A: Fast Scan (ms)"]
        S1["scan_project"]
        S2["total_symbols"]
        S3["module_tree"]
        S4["entry_points"]
    end

    subgraph B["Phase B: Background Enhance (async, seconds)"]
        E1["enhance_project"]
        E2["full tree-sitter"]
        E3["call graph"]
        E4["FTS index"]
        E5["semantic_fact (v0.3)"]
    end

    A -->|"trigger"| B

Loading

---

3. 8-Layer Smart Filtering: Why Only 6,029 of 36,919 Files Are Indexed

CodeScope does not index every file in a project. Instead, it applies an 8-layer cascade that strips away noise so you only see what matters: the core source code.

The Problem

A typical project looks like this (rustc, the Rust compiler):

Total source files:  36,919
  tests/            26,293  ← 71%: test suites
  src/tools/*/test/  3,802  ← 10%: embedded test directories
  library/*/test/      339  ←  1%: library tests
  compiler/*/test/     118  ← <1%: compiler tests
  docs/vendor/bench/   368  ←  1%: documentation, vendored deps, benchmarks
  ─────────────────────────────────────
  Core code indexed: 6,029  ← 16%: the actual source code

Without filtering, CodeScope would waste 84% of its time indexing tests, vendored dependencies, documentation, and build artifacts — files no one needs to analyze.

The 8-Layer Filter Cascade

Layer 1: any-depth skip directories  (~120 patterns)
  .git, .svn, .hg, node_modules, .venv, target, build, dist,
  vendor, __pycache__, .github, deploy, docker, k8s, ...
  → Catches VCS, build artifacts, dependencies, CI/CD, infra at ANY depth

Layer 2: top-only skip directories  (depth ≤ 3, Java-safe)
  test, tests, docs, examples, samples, scripts, e2e, integration,
  assets, static, public, media, i18n, bench, benchmarks, ...
  → For Java: protects package namespaces (org/.../samples/petclinic)

Layer 3: file suffix skip  (always applied)
  .md, .txt, .json, .yaml, .toml, .ini, .png, .jpg, .svg,
  .pdf, .zip, .tar, .min.js, .d.ts, ...
  → Non-source files, documentation, images, archives

Layer 4: exact filename skip
  package-lock.json, yarn.lock, .DS_Store, Thumbs.db,
  .env, .env.local, .gitkeep, .gitignore, ...

Layer 5: filename/directory prefix skip
  File prefixes: ._*, ~$*, #*#
  Directory prefixes: build_*, test_*, tmp_*

Layer 6: .gitignore pattern matching
  Respects every rule in the project's .gitignore

Layer 7: .codescopeignore (user-defined)
  Additional custom ignore patterns per project

Layer 8: file size limit + language detection
  • Max file size (default 10 MB, configurable via CODESCOPE_MAX_FILE_SIZE)
  • Undetectable language files are silently skipped

Real-World Impact

Project	Raw Source Files	After Filtering	Filtered Out	Time Saved
rustc (Rust compiler)	36,919	6,029	84%	~2.5 min
CodeScope (self)	356	168	53%	~1 s

Override: force_index_files

Need to index a specific test file or vendored directory? Use the force_index_files MCP tool — it bypasses all 8 layers:

codescope cli force_index_files '{"paths":["/path/to/test/file.rs"]}'

---

4. Quick Start

Prerequisites

Platform	Dependencies
macOS	Xcode CLT, cmake, Rust (1.85+)
Linux	build-essential, cmake, Rust (1.85+)
Windows ⚠️ Beta	MinGW-w64 14.0.0+, Rust x86_64-pc-windows-gnu target, cmake. Every graph-query tool (shortest_path, get_neighbors, get_callers/callees, graph_query, subgraph, entry_points, trace_path, hotspots, impact_analysis, ...) works via the built-in SQLite graph-query backend (CSR adjacency, sub-millisecond call-graph lookups).

Install Pre-built Binary

curl -fsSL https://raw.githubusercontent.com/Timwood0x10/CodeScope/main/install.sh | bash
export PATH="$PATH:$HOME/.codescope/bin"

macOS code signing issue: If the binary is killed immediately on launch (exit code 137 / SIGKILL), re-sign it locally:

codesign --sign - --force ~/.codescope/bin/codescope

This happens because the CI-built binary uses ad-hoc signing, which newer macOS versions may reject. Re-signing with your local machine's identity resolves it.

Build from Source

git clone https://github.com/Timwood0x10/CodeScope.git
cd CodeScope

# macOS:
brew install llvm@21 cmake pkg-config
cargo build --release

# Linux (Ubuntu):
sudo apt-get install -y build-essential cmake llvm-dev libclang-dev
cargo build --release

Index and Query

# Index a project
codescope cli index_project '{"project_path":"/path/to/your/project"}'

# Quick overview
codescope cli project_overview '{}'

# Start MCP server (for AI clients)
codescope

Large Projects

For projects with thousands of files, use the built-in parallel scheduler:

codescope index-parallel /path/to/large/project

---

5. MCP Tools (47 Tools)

Indexing

Tool	Description	Parameters
index_project	Index a project directory: parse all source files, build IR, and construct the code graph.	{"project_path": "string (required)", "language_filter": "string (optional)"}
index_file	Index a single source file.	{"file_path": "string (required)"}
force_index_files	Force-index files/dirs bypassing default skip rules (test/, docs/, node_modules/, .gitignore, etc.).	{"paths": ["string (required)"], "language_filter": "string (optional)"}

Project Overview

Tool	Description	Parameters
project_overview	Primary — comprehensive project overview: languages, modules, symbols, entry points, analysis progress.	{}
get_graph_stats	Quick statistics: nodes, edges, files.	{}
get_module_tree	Hierarchical module/directory tree.	{}
get_entry_points	Find entry points (main/init/setup/run/handler).	{}
get_routes	Get registered HTTP routes (Gin/Echo/Chi/net/http).	{}
get_type_info	Query type definitions (struct/enum/trait) with reference counts.	{"type_name": "string (optional)"}

Symbol Lookup

Tool	Description	Parameters
find_symbol	Recommended — find symbol by exact name (kind, file, line/col).	{"symbol_name": "string (required)"}
find_references	Find all locations referencing a symbol.	{"symbol_name": "string (required)", "file_filter": "string (optional)"}
explain_symbol	Get comprehensive symbol info: definition, callers, callees, dependencies.	{"symbol_name": "string (required)"}
find_definition	[DEPRECATED — use find_symbol]	{"symbol_name": "string (required)"}

Call Graph

Tool	Description	Parameters
find_callers	Find who calls a function.	{"symbol_name": "string (required)", "file_filter": "string (optional)"}
find_callees	Find what a function calls.	{"symbol_name": "string (required)", "file_filter": "string (optional)"}
find_callers_by_entity	Find callers of a symbol by its graph entity id.	{"entity_id": "integer (required)"}
find_callees_by_entity	Find callees of a symbol by its graph entity id.	{"entity_id": "integer (required)"}
get_verifier_registry_status	Inspect the registered verifiers and their health (supported claim types, unsupported list, backend readiness).	{}
codescope_trace	Interactive recursive call exploration (depth + direction) or shortest path.	`{"function_name": "string", "depth": "integer (default 1, max 5)", "direction": "callers
trace_flow	Recursive execution flow tracing (caller→callee chain).	{"function_name": "string (required)", "depth": "integer (default 3, max 10)"}
shortest_path	Shortest call path between two functions (BFS).	{"from": "string", "to": "string", "from_id": "integer", "to_id": "integer"}
connected_components	Connected components in the call graph.	{}

Graph Query

Tool	Description	Parameters
graph_query	Cypher-like DSL query: MATCH (Function:main)-[Calls]->(Method).	{"dsl": "string (required)"}
get_graph	Retrieve the complete code graph in paginated pages.	{"node_offset": "integer", "node_limit": "integer (max 50000)", "edge_offset": "integer", "edge_limit": "integer (max 200000)", "node_types": "string", "edge_types": "string"}
get_subgraph	Fetch a local region centered on a node (1-hop).	{"node_id": "integer (required)", "radius": "integer", "node_types": "string", "edge_types": "string"}
get_neighbors	Fetch direct neighbors (callers + callees) of a graph node.	{"node_id": "integer (required)", "edge_type": "integer (default -1)", "radius": "integer"}

Search

Tool	Description	Parameters
search	Recommended — unified search: FTS5 exact/prefix matching complemented by n-gram semantic vector search (restored in v0.2.5; lexical similarity, no external model) when results run short.	{"query": "string (required)", "limit": "integer (default 20, max 100)"}
search_code	[DEPRECATED — use search]	{"query": "string (required)", "limit": "integer"}

Verification

Tool	Description	Parameters
verify_integrity	Check README-promised features actually exist in code.	{}
verify_claim	Verify a single claim (capability_exists / contract_holds / architecture_follows).	{"claim": "string (required)"}
verify_summary	Parse natural-language summary and verify each claim.	{"text": "string (required)"}
verify_review	Verify code review comment claims.	{"text": "string (required)"}
verify_reality	Verify a single AI statement against code evidence.	{"text": "string (required)"}

Evidence Pipeline (v0.3)

The v0.3 Evidence Pipeline transforms indexed code into verifiable evidence and project health snapshots. Flow: Facts → SemanticFacts → Evidence → Verification → ProjectState. Semantic facts are extracted by enhance_project (Step 1.5); evidence is built by applying declarative rule files (engine/src/evidence/rules/*.json) to the semantic_fact table.

Tool	Description	Parameters
enhance_project	Run background enhancement: full tree-sitter parse, call graph, FTS, and v0.3 semantic_fact extraction. Prerequisite for build_evidence to produce non-empty findings. Complexity metrics and n-gram semantic vectors are built during index_project (restored in v0.2.5).	{}
build_evidence	Build evidence findings by applying the rule set (sync/memory/error/pattern/framework/ffi) to the project's semantic_fact rows. Each rule declares fact needs + a combine mode (Collect / MissingMatch / MissingMatchPerFunction / Count). Returns a JSON array of Evidence objects. Run after enhance_project so semantic facts are populated.	`{"category": "string (optional, one of: sync
verify_statement	Verify a natural-language claim against the project's indexed evidence. Pipeline: IntentParser → Planner → EvidenceBuilder → VerdictBuilder. Returns JSON with verdict (Supported|Contradicted|PartiallyVerified|Unknown), confidence, requirements[], and evidence[]. Use this for yes/no questions about code behavior (e.g. "does this project safely handle CString?").	{"claim": "string (required)"}
build_project_state	Build (or rebuild) and persist the project state snapshot. Runs the full v0.3 Evidence Pipeline (evidence aggregation + state queries) and UPSERTs the result into the project_state table. Returns the snapshot JSON: overall confidence, capability/architecture/workflow/dead_code scores, per-category issue counts, and last_updated timestamp.	{}
get_project_state	Get the previously persisted project state snapshot (without rebuilding). Returns the snapshot_json string for the project, or a JSON error object if no snapshot exists yet (run build_project_state first). Use this for fast reads of the latest health snapshot.	{}

Drift Detection

Tool	Description	Parameters
detect_drift	Scan all declared capabilities & contracts for doc-vs-code drift.	{}
detect_documentation_drift	Check README language claims vs actual code entities.	{}
detect_capability_drift	Check declared capabilities have implementing entities.	{}
detect_architecture_drift	Check call edges for layer violations (Repository→Controller).	{}

Change Impact & Module

Tool	Description	Parameters
detect_changes	Analyze impact of modified files: direct/indirect callers.	{"modified_files": "string (required)"}
explain_module	Build module knowledge card: entities, capabilities, integrity score.	{"module_name": "string (required)"}

Utilities

Tool	Description	Parameters
detect_ffi_boundaries	Detect FFI boundaries (extern/C, JNI, WASM, C ABI).	{}
count_tokens	Estimate token count (DeepSeek formula).	{"text": "string (required)"}

Quick Decision Guide

New project       → project_overview
Module structure  → get_module_tree
Entry points      → get_entry_points
Search code       → search
Call chain        → find_callers / find_callees
Deep dive symbol  → explain_symbol
HTTP routes       → get_routes
Type info         → get_type_info
Verify claim      → verify_claim
Enhance project   → enhance_project
Verify statement  → verify_statement
Build evidence    → build_evidence
Project health    → build_project_state
Detect drift      → detect_documentation_drift
Change impact     → detect_changes

---

6. Knowledge Graph

CodeScope builds a module-level knowledge graph as a side product of the verification pipeline. It learns structured metadata about how the project is organized, what's important, what's redundant, and what it promises:

Layer	Table	What it tells you
Call graph	relation, architecture_edge	Cross-module call dependencies; drives detect_architecture_drift
Module health	module_summary	Per-module incoming_count / outgoing_count / dead_entities / utilization / role
Module dependency	architecture_edge, module_edge	"Change module A → these modules depend on it"
Documented capability	capability + document	README-extracted capabilities; drives detect_capability_drift / verify_claim

All knowledge-layer tables are directly queryable via get_knowledge_graph:

get_knowledge_graph {"table":"architecture_edge","limit":5}
// → {"table":"architecture_edge","rows":[...],"total":3351}

get_knowledge_graph {"table":"capability","limit":10}
// → {"table":"capability","rows":[...],"total":3}

Supported tables: entity, relation, architecture_edge, module_edge, capability, document, module_summary.

---

7. Benchmark

All benchmarks measured on Apple M3 Max (36 GB RAM, 14 cores), macOS, 2026-08-14, using target/release/codescope (v0.2.6) in worker (serial full index) mode with the pure-SQLite graph backend (no LadybugDB/Kuzu dependency), CODESCOPE_INDEX_MODE=normal. Query latency measured via MCP server mode (engine initialized once, median of 7 runs). Numbers reflect the in-memory fuzzy resolver + ordering fix (edge count 1,249 → 1,189 vs. the pre-fix binary; nodes/files unchanged). Other hardware will produce different results — expect slower performance on less capable machines.

Index Time

Project	Language	Files	Nodes	Edges	Index Time	Peak RSS
CodeScope (self)	C++/Rust	197	1,509	1,189	0.95 s	~179 MB
tinygo	Go	812	21,557	4,485	1.77 s	~505 MB
rustc (Rust compiler, monorepo)	Rust	5,575	130,410	117,284	38.94 s	~4.13 GB

Query Latency

All graph queries run on the built-in SQLite graph-query backend (CSR adjacency tables), sub-millisecond for typical call-graph lookups. Measured on the CodeScope self-index DB unless noted.

Query	Measured (median)
get_graph_stats	0.08 ms
find_callers("parse")	0.16 ms
find_callees("parse")	0.17 ms
graph_query (LIMIT 100)	88.8 ms
graph_query (full scan, no LIMIT, self DB)	88.9 ms
graph_query (full scan, rustc DB)	>180 s — always use LIMIT on large graphs
shortest_path	0.09 ms (rustc DB: 0.38 ms)
get_neighbors	0.06 ms (rustc DB: 2.36 ms)
get_subgraph	0.10 ms (rustc DB: 5.68 ms)
get_module_tree	0.08 ms
get_entry_points	0.21 ms
get_knowledge_graph	0.10 ms

Micro Benchmarks

Measured on the self-index DB via MCP server mode (engine initialized once).

Metric	Value
Engine init (GraphStore::open)	3 ms
Index throughput (CodeScope self)	~207 files/s (197 files / 0.95 s)
Symbol query (find_callers/find_callees, MCP-level)	0.16–0.17 ms
graph_query (LIMIT 100)	88.8 ms
10 queries (total, MCP-level)	~89.9 ms (dominated by graph_query)
Query latency (CLI, includes process start)	10–17 ms

Cross-File Resolution

Project	Cross-File CALLS	% of total CALLS
CodeScope (C++)	727	61.1%
tinygo (Go)	2,210	49.3%
rustc (Rust)	70,634	60.2%

Fast Scan (Lightweight, ms-level)

codescope discover（File discovery + module statistics, pure Rust, no engine initialization）。

Project	Time	Languages	Modules
CodeScope (self)	27 ms	cpp, rust, c	engine 290 / server 20

Token Savings

Using code graphs instead of raw source files saves ~98.9% tokens on average:

Scenario	Raw Source	CodeScope	Savings
Find function definition	~2,265 tokens	~21 tokens	99.1%
Trace function callers	~2,000 tokens	~18 tokens	99.1%
Project architecture overview	~1,875 tokens	~32 tokens	98.3%
USB subsystem overview	~24,000 tokens	~250 tokens	99.0%
Scheduler analysis	~15,000 tokens	~180 tokens	98.8%

---

8. Skills (Shell Wrappers)

The skills/ directory provides shell scripts that wrap common CodeScope queries so you don't need to remember the JSON schema:

cd CodeScope

# Index a project
./skills/index.sh ~/path/to/project

# One-shot full analysis report
./skills/analyze.sh ~/path/to/project

# Graph statistics
./skills/stats.sh

# Module tree
./skills/modules.sh

# Trace call path A → B
./skills/trace.sh func_a func_b

# Top 20 hotspots
./skills/hotspots.sh 20

# Browse architecture dependencies
./skills/knowledge.sh architecture_edge 20

Each script calls codescope cli <tool_name> '<json_args>' internally. See skills/skills.md for the full reference.

---

9. Environment Variables

Variable	Default	Description
CODESCOPE_DB_PATH	.codescope/codescope.db	SQLite database path
CODESCOPE_INDEX_MODE	normal	Index mode: fast / normal / strict
CODESCOPE_EXCLUDE_PATHS	(unset)	Comma-separated glob patterns to exclude
CODESCOPE_WORKERS	min(hw,8)	Total parse-worker cores for index-parallel (kDefaultParseWorkers=8)
CODESCOPE_WORKER_TIMEOUT	300	Worker subprocess timeout in seconds
CODESCOPE_MAX_FILE_SIZE	(unset)	Max source file size to index in bytes
CODESCOPE_MMAP_SIZE	256 MB	SQLite mmap_size pragma value
CODESCOPE_MEM_LIMIT_MB	4096	Dynamic-scheduler memory ceiling
CODESCOPE_DYNAMIC_SCHED	auto	Dynamic CPU scheduling: 1 on, 0 off, unset = auto
CODESCOPE_VERBOSE	0	Set to 1 for verbose logging
CODESCOPE_LSP	(unset)	LSP server command for type enhancement

---

10. License

Apache 2.0 — see LICENSE.

CodeScope v0.2.6 — Built with Rust 2024 + C++23 + tree-sitter + SQLite.