Code Intelligence & Brain Mode

Cora includes a built-in symbol index, call graph, and hybrid semantic search engine. No external services required — everything runs locally.

Quick Start

bash

# 1. Index your project (extracts symbols, builds vector index)
cora index

# 2. Search symbols (keyword)
cora explore "authenticate"

# 3. Semantic search (hybrid: keyword + vector + graph)
cora brain "error handling pattern"

# 4. Trace call chains
cora trace main

# 5. View architecture overview
cora arch

Indexing

`cora index`

Scans your project, extracts symbol definitions (functions, structs, enums, traits, etc.), and builds:

Component	Technology	Storage
Symbol table (regex)	Regex extractors (15 languages)	SQLite FTS5
Symbol table (AST)	Tree-sitter grammars (12 languages, opt-in)	SQLite FTS5
Vector embeddings	Static hashing (256d) or pretrained nomic (768d), runtime-selectable	usearch HNSW index
Call graph	Regex scope tracking + tree-sitter AST edges	SQLite `edges` table

bash

cora index              # Index current project (incremental)
cora index --rebuild    # Drop and re-index from scratch
cora index --stats     # Show index statistics
cora index --watch     # Watch for file changes and auto-update
cora index --prune     # Remove symbols from deleted files

Supported Languages

Cora extracts symbols using two strategies — regex (always available) and tree-sitter AST (opt-in via --features tree-sitter at build time):

	Regex Extraction	AST (Tree-sitter)
Rust	✅	✅
Go	✅	✅
Python	✅	✅
TypeScript/TSX	✅	✅
Svelte	✅	✅ (via TypeScript)
Java	✅	✅
C	✅	✅
C++	✅	✅
C#	✅	✅
Ruby	✅	✅
PHP	✅	✅
Scala	✅	✅
JavaScript	✅	✅
Swift	✅	—
Kotlin	✅	—
Dart	✅	—
Lua	✅	—
Zig	✅	—

Regex-only languages work out of the box. For AST-accurate extraction (full call graph, precise imports/exports), build with tree-sitter:

bash

cargo install --git https://github.com/codecoradev/cora-code --features tree-sitter

Multi-Project Index

All projects share a single global database:

~/.codecora/cora-code/
├── graph.db              # SQLite — symbols, FTS5 index, call edges
└── cora_index.usearch   # usearch HNSW — 256d vector embeddings

Index multiple repos and they all become searchable from any directory:

bash

cd ~/repos/my-api && cora index        # Index Go project
cd ~/repos/my-app && cora index        # Index Flutter project
cd ~/repos/my-lib && cora brain "auth" # Results from ALL indexed projects

Environment Override

bash

CODECORA_HOME=/custom/path cora index  # Use custom data directory

Search Commands

`cora explore` — Keyword Search

FTS5 full-text search over symbol names and signatures.

bash

cora explore "authenticate"         # Search by name
cora explore --kind function        # Filter by symbol kind
cora explore --language rust        # Filter by language
cora explore --limit 20              # Max results
cora explore --json                 # JSON output

`cora brain` — Hybrid Semantic Search

Combines three search signals into ranked results via Reciprocal Rank Fusion (RRF, k=60):

Signal	Engine	What it finds
FTS5	SQLite keyword match	Exact name/signature matches
Vector KNN	usearch HNSW (cosine)	Semantically similar code
Graph BFS	Call graph traversal	Related symbols (callers/callees)

bash

cora brain "error handling"              # Top 20 results
cora brain "TokenEmbedding" --json       # JSON output
cora brain "parsing" --limit 10          # Custom limit

JSON Output

json

[
  {
    "symbol_id": 935,
    "name": "normalize_error_handling",
    "kind": "function",
    "file": "src/engine/debt_tracker.rs",
    "line": 685,
    "score": 0.0164,
    "signals": ["fts"]
  }
]

The signals field shows which search signals matched: "fts", "vector", "graph", or combinations like ["fts", "vector"].

Embedding Engine

Cora supports multiple embedding backends, selectable at runtime via brain.embedding in .cora.yaml. No recompilation needed to switch.

Backend	Dimensions	Method	Feature Flag	When to use
`hashing`	256	Bag-of-tokens hashing	Always available	Zero-dependency, fast, good for near-duplicate detection
`pretrained`	768	Nomic-embed-code distilled	`pretrained-embed`	Better semantic matching, real code embeddings
`auto` (default)	—	Picks best available	—	Uses `pretrained` if compiled, falls back to `hashing`

yaml

# .cora.yaml
brain:
  embedding: auto   # auto | hashing | pretrained

Note: 256d and 768d embeddings cannot be mixed in the same index. Changing the backend requires cora index --rebuild. Future phases will add ONNX-based embedding models (see Roadmap).

Call Graph Commands

`cora callers` — Who Calls This?

Find all symbols that call a given symbol.

bash

cora callers "authenticate"    # Who calls authenticate?
cora callers --json            # JSON output
cora callers --limit 50        # Max results

`cora impact` — What Breaks?

Analyze the blast radius of changing a symbol.

bash

cora impact "parse_response"          # What depends on this?
cora impact "parse_response" --depth 3  # 3 levels up the call graph
cora impact --json                     # JSON output

`cora trace` — Call Chain Tracing

Trace execution paths through the call graph.

bash

cora trace "main"                    # Trace outward (callees)
cora trace "handle_request" --incoming  # Trace inward (callers)
cora trace "process" --depth 4         # Limit traversal depth
cora trace --json                     # JSON output

Requires schema v3 edges table. When built with --features tree-sitter, Cora uses AST-based edge extraction for more accurate call graphs. Regex-only builds still generate edges via scope tracking.

bash

# Build with tree-sitter for best call graph accuracy
cargo install --git https://github.com/codecoradev/cora-code --features tree-sitter
cora index --rebuild  # Re-index to get AST edges

`cora arch` — Architecture Overview

Display a high-level view of the codebase structure.

bash

cora arch          # Human-readable overview
cora arch --json   # JSON output

Shows: module breakdown, edge types (calls, imports), and top connector symbols.

`cora dead-code` — Dead Code Detection

Find functions and methods that have zero callers — candidates for removal.

bash

cora dead-code                     # Find dead functions
cora dead-code --include-tests     # Include test functions (test_*, *_test)
cora dead-code --min-lines 10      # Filter out tiny functions
cora dead-code --json              # JSON output

Tip: Use analysis.entry_point_patterns in .cora.yaml to mark entry points (e.g. *Handler, main) so they're not flagged as dead code.

`cora query` — Code Graph Query

Query the call graph with simple pattern syntax.

bash

cora query "main -> *"             # What does main call?
cora query "* -> authenticate"     # What calls authenticate?
cora query "MyStruct"              # Find all edges involving MyStruct
cora query --limit 100 "main -> *"

Pattern syntax: source -> target, where each side can be a symbol name or * (wildcard).

`cora routes` — HTTP Route Listing

List detected HTTP routes from framework annotations. Supports Axum, Actix, Express, FastAPI, Flask, and Go (net/http, gin, echo, chi).

bash

cora routes                        # All routes
cora routes --method GET           # Filter by HTTP method
cora routes --prefix /api          # Filter by path prefix
cora routes --json                 # JSON output

Test Impact Analysis

`cora affected`

Find tests that are impacted by changed files.

bash

cora affected                              # From git diff
cora affected src/auth.rs src/api.rs      # Specific files
cora affected --stdin                      # Pipe from git diff --name-only
cora affected --filter "*test*"            # Custom test file pattern
cora affected --json                       # JSON output

MCP Integration

All code intelligence features are available as MCP tools for AI coding agents:

Tool	Description
`cora.search_symbols`	FTS5 symbol search
`cora.find_callers`	Find callers of a symbol
`cora.find_impact`	Impact analysis
`cora.find_affected_tests`	Test impact analysis
`cora.index_status`	Index statistics
`cora.brain_search`	Hybrid semantic search
`cora.get_project_info`	Project metadata & config
`cora.get_memory`	Review memory recall

Data Directory

~/.codecora/cora-code/
├── cora.db               # SQLite database (renamed from graph.db in v0.9)
│   ├── projects         # One row per indexed project
│   ├── symbols          # All symbols from all projects
│   ├── symbols_fts      # FTS5 virtual table for keyword search
│   ├── edges            # Call relationships (caller_id → callee_id)
│   ├── reviews          # Review history for tech debt tracking
│   └── findings         # Review findings + finding_events
└── cora_index.usearch   # usearch HNSW vector index
    ├── cora_index.usearch.keys    # Key-to-symbol-id mapping
    └── cora_index.usearch.lock    # File lock (fs2)

To reset everything:

bash

rm -rf ~/.codecora/cora-code/*
cora index --rebuild

Schema Versioning

The database uses automatic migrations. Current schema version: v7.

Version	Changes
v1	Initial symbols table + FTS5
v2	Added language column
v3	Added `edges` table for call graph
v4	Added `embedding_tier`, `embedding_dims`, `embedding_model`, `last_embedded_at` to projects
v5	Added `reviews`, `findings`, `finding_events` tables for review history and findings tracking
v6	Added index config hash column for fingerprint invalidation on config changes; rebuilt FTS5 with `file` column for camelCase search
v7	Added `embed_fingerprint TEXT` column to `symbols` for incremental per-symbol embedding

Code Intelligence & Brain Mode ​

Quick Start ​

Indexing ​

cora index ​

Supported Languages ​

Multi-Project Index ​

Environment Override ​

Search Commands ​

cora explore — Keyword Search ​

cora brain — Hybrid Semantic Search ​

JSON Output ​

Embedding Engine ​

Call Graph Commands ​

cora callers — Who Calls This? ​

cora impact — What Breaks? ​

cora trace — Call Chain Tracing ​

cora arch — Architecture Overview ​

cora dead-code — Dead Code Detection ​

cora query — Code Graph Query ​

cora routes — HTTP Route Listing ​

Test Impact Analysis ​

cora affected ​

MCP Integration ​

Data Directory ​

Schema Versioning ​

Code Intelligence & Brain Mode

Quick Start

Indexing

`cora index`

Supported Languages

Multi-Project Index

Environment Override

Search Commands

`cora explore` — Keyword Search

`cora brain` — Hybrid Semantic Search

JSON Output

Embedding Engine

Call Graph Commands

`cora callers` — Who Calls This?

`cora impact` — What Breaks?

`cora trace` — Call Chain Tracing

`cora arch` — Architecture Overview

`cora dead-code` — Dead Code Detection

`cora query` — Code Graph Query

`cora routes` — HTTP Route Listing

Test Impact Analysis

`cora affected`

MCP Integration

Data Directory

Schema Versioning