How to Index a Project with the Native SCIP Pipeline¶

Index a project's source code into the LadybugDB (formerly Kuzu) code-graph so that amplihack query-code can answer structural questions about it.

Before you start¶

You need:

amplihack binary built and on PATH (cargo build --release)
At least one SCIP indexer installed for the languages in your project (see the table in SCIP indexer prerequisites)
The project checked out locally with source files present

Run amplihack doctor to see which prerequisites are met.

Steps¶

1. Verify at least one indexer is available¶

amplihack doctor

Look for lines like ✓ scip-python or ✓ rust-analyzer. If none appear, install the relevant indexer before continuing.

# Example: install scip-python (Go binary, despite the name)
pip install scip-python

# Example: install scip-typescript
npm install -g @sourcegraph/scip-typescript typescript

2. Run the indexer¶

From the project root:

amplihack index-scip

The command auto-detects which languages are present and runs the available indexers. Example output for a Python + Rust project:

Native SCIP indexing summary
========================================
Success: true
Completed: python, rust
Artifact: /home/user/myproject/.amplihack/indexes/python.scip
Artifact: /home/user/myproject/.amplihack/indexes/rust.scip
Imported: files=89, classes=24, functions=412, imports=156, relationships=538

If a language's indexer is not installed, it is skipped with a note in the Skipped: line — this is not an error.

3. Confirm the graph has data¶

amplihack query-code stats

Expected output:

Code Graph Statistics:
  Files:     89
  Classes:   24
  Functions: 412
  Memory→File links:     7
  Memory→Function links: 3

If all counts are 0, the indexer ran but produced no output (check the Skipped: or Failed: lines from step 2).

4. Query the graph¶

# List all functions in a specific file
amplihack query-code functions --file code_graph

# Find what calls a function
amplihack query-code callers run_tui

# Search for any symbol by name
amplihack query-code search FleetTui

# Get machine-readable output
amplihack query-code --json stats

See the query-code reference for all available subcommands.

Index a specific path (not the current directory)¶

amplihack index-scip --project-path /path/to/other/project

Index only selected languages¶

# Index only Rust and Go, skip Python even if present
amplihack index-scip --language rust --language go

Re-index after code changes¶

Run amplihack index-scip again. All upserts are idempotent — existing nodes are updated in place and no duplicates are created.

Import a pre-existing blarify.json¶

If you have a blarify.json from a CI artifact or another tool:

amplihack index-code /path/to/blarify.json

The JSON is parsed and merged into the same LadybugDB graph that index-scip populates. If the file is absent, the command logs a warning and exits 0 — it does not abort.

Troubleshoot: "no supported source files found"¶

index-scip scans for files with known extensions (.py, .rs, .ts, etc.) and skips node_modules, .git, .venv, and similar directories. If your project uses non-standard extensions or is entirely in a language that is not yet supported, the scan finds nothing.

Run with --language to specify a language explicitly:

amplihack index-scip --language python

If the language scan should have found files but did not, check that the project root contains source files at the top level or in subdirectories (the scan is recursive).

Troubleshoot: "native SCIP indexing did not complete successfully"¶

This exit-1 error means no language completed successfully (all either failed or were skipped). Common causes:

Cause	Fix
Indexer binary not on PATH	Install the binary; check with `amplihack doctor`
`index.scip` not written	The indexer ran but produced no output; check its stderr
Graph DB path not writable	Ensure `<project>/.amplihack/` is writable