Paths: File paths are relative to skills repo root.

Code Knowledge Graph

Type: Standalone Utility Category: 0XX Dev Environment

Indexes codebase into a layered graph (tree-sitter AST → SQLite) and provides dependency analysis, path tracing, references, implementations, and architecture overview via MCP tools.

Inputs

Input	Required	Source	Description
`project_path`	yes	args or CWD	Project root to index
`command`	no	args	Specific action: `index` , `search` , `symbol` , `paths` , `refs` , `arch`

When to Use

Starting work on an unfamiliar codebase →
```
index
```
+
```
architecture
```
Before refactoring a function/class →
```
search
```
+
```
get_symbol
```
+
```
trace_paths
```
Understanding call flow →
```
trace_paths
```
Finding a symbol quickly →
```
search
```

Workflow

Phase 1: Index

Check if graph exists (

.hex-skills/codegraph/index.db

in project root).

If NOT exists:

Call: index_project({ path: "{project_path}" })

If exists (re-index on demand):

Call: index_project({ path: "{project_path}" })

Idempotent — skips unchanged files automatically.

Phase 2: Query

Route based on user intent:

User says	Tool	Parameters
"Show dependencies" / "What uses X?"	`trace_paths`	`{ name: "X", file: "...", path_kind: "mixed", direction: "reverse", path: "{project_path}" }`
"Who calls X?" / "What does X call?"	`trace_paths`	`{ name: "X", file: "...", path_kind: "calls", direction: "reverse"\|"forward", path: "{project_path}" }`
"Tell me about X" / "Context of X"	`get_symbol`	`{ name: "X", file: "...", path: "{project_path}" }`
"Project structure" / "Architecture"	`get_architecture`	`{ path: "{project_path}", scope?: "src/" }`
"Find symbol X"	`search_symbols`	`{ query: "X" }`
"Watch for changes"	`watch_project`	`{ path: "{project_path}" }`
"Find duplicate code"	`find_clones`	`{ path: "{project_path}", type: "all" }`
"Risky hotspots"	`find_hotspots`	`{ path: "{project_path}", min_callers: 2, min_complexity: 5 }`
"Unused exports"	`find_unused_exports`	`{ path: "{project_path}" }`
"Circular dependencies"	`find_cycles`	`{ path: "{project_path}" }`
"Module coupling"	`get_module_metrics`	`{ path: "{project_path}", min_coupling: 0 }`
"Implementations / overrides"	`find_implementations`	`{ name: "X", file: "...", path: "{project_path}" }`
"Dataflow / propagation"	`find_dataflows`	`{ source: { symbol: { name: "X", file: "..." }, anchor: { kind: "param", name: "input" } }, sink?: { symbol: { name: "X", file: "..." }, anchor: { kind: "return" } }, path: "{project_path}" }`

Canonical selector rule: Semantic tools accept exactly one selector:

```
symbol_id
```
```
workspace_qualified_name
```
```
qualified_name
```
```
name
```
+
```
file
```

Preferred flow: use

search_symbols

first, then feed the returned

workspace_qualified_name

into

get_symbol

trace_paths

find_references

, or

find_implementations

for exact follow-up queries.

Dataflow anchors:

find_dataflows

requires

source.anchor

and optional

sink.anchor

. Use:

```
param
```
for function parameters
```
local
```
for local variables
```
return
```
for function returns
```
property
```
with
```
access_path
```
for bounded property flow

Precision controls:

get_symbol

trace_paths

, and

find_references

support

min_confidence

(

low

inferred

exact

precise

) when the caller wants to suppress weaker parser-only facts.

Phase 3: Present Results

Show MCP tool output directly (markdown tables)
For code snippets referenced in results, use
```
hex-line read_file
```
with line ranges
Suggest follow-up queries based on results:
- After
```
search_symbols
```
  → suggest
```
get_symbol
```
  with
```
workspace_qualified_name
```
  for the top exact match
- After
```
get_symbol
```
  → suggest
```
trace_paths
```
  if refactoring
- After
```
trace_paths
```
  → suggest
```
find_references
```
  or
```
find_implementations
```
  depending on symbol kind

Supported Languages

Language	Extensions	Coverage
JavaScript	.js, .mjs, .cjs, .jsx	Strongest semantic coverage
TypeScript / TSX	.ts, .tsx	Strongest semantic coverage
Python	.py	Workspace-aware definitions, calls, imports, unused exports; optional precise overlay when provider is installed
C#	.cs	Workspace-aware definitions, calls, project/namespace ownership, type relations; optional precise overlay when provider is installed
PHP	.php	Workspace-aware definitions, calls, PSR-4 namespace imports, unused exports; optional precise overlay when provider is installed

MCP Server Setup

Add to

.mcp.json

json

{
  "mcpServers": {
    "hex-graph": {
      "command": "node",
      "args": ["{skills_repo}/mcp/hex-graph-mcp/server.mjs"]
    }
  }
}

Definition of Done

Project indexed (index_project returns success)
Query results shown to user
Follow-up suggestions provided

Version: 0.1.0 Last Updated: 2026-03-20

ln-020-codegraph

NPX Install

Tags

SKILL.md Content