CLI Commands

SYNAPSEED provides a CLI for standalone analysis and MCP server operation.

Global Options

synapseed [OPTIONS] <COMMAND>

Options:
  -p, --project <PATH>   Project root directory [default: .]
  -h, --help             Print help
  -V, --version          Print version

Commands

hoist

Index a project and display its code graph skeleton.

synapseed hoist --project /path/to/project

Output: JSON with files_indexed and symbols_indexed counts.

---

lookup <NAME>

Look up a symbol by name across the indexed project.

synapseed lookup --project . MyStruct

Output: JSON array of matching symbols with file path, line numbers, kind, and signature.

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scan

Scan content for sensitive data (DLP check).

# From argument
synapseed scan --text "api_key=sk-live-abc123"

# From stdin
echo "secret_token=ghp_xxxx" | synapseed scan

Output: CLEAN or ALERT with redacted content.

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check <COMMAND>

Evaluate a shell command against the security sentinel.

synapseed check "cargo test"
# ALLOWED (Safe): cargo test

synapseed check "rm -rf /"
# DENIED: Matches destructive pattern

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diagnose

Run full system diagnostic.

synapseed diagnose --project .

Output: Project state, DNA configuration, git status, and metrics.

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history

Show git history summary and recent commits.

synapseed history --project . --limit 10

Options:

• --limit, -l <N> — Number of recent commits (default: 10)

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blame <FILE>

Show blame information for a file region.

synapseed blame --project . src/main.rs --start 1 --end 20

Options:

• --start, -s <LINE> — Start line (default: 1)
• --end, -e <LINE> — End line (default: 20)

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status

Show runtime metrics and system status.

synapseed status --project .

Initializes core plugins and displays all metrics.

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init

Initialize all plugins and broadcast SystemInit event.

synapseed init --project .

Useful for testing plugin initialization and event flow.

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serve

Start MCP server (JSON-RPC 2.0 over stdio).

synapseed serve --project .

This is the primary mode for LLM integration. All output goes to stderr; stdout is reserved for JSON-RPC.

Environment Variables

Variable	Description
RUST_LOG	Log level (default: info)
SYNAPSEED_SELF_TELEMETRY	Set to 1 for self-instrumentation

---

ask <QUERY>

Ask a natural-language question — SYNAPSEED orchestrates all subsystems (compiler, search, history, security, architecture) and returns enriched context.

synapseed ask "why is the login broken?"

# With Direct Symbol Injection (source code in prompt)
synapseed ask --raw "explain the router module"

Options:

• --raw — Inject the exact source code of discovered symbols into the prompt

Aliases: ask_synapseed, whisper

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search <QUERY>

Search for code by concept using the Tantivy keyword index.

synapseed search "authentication flow" --limit 10

Options:

• --limit, -l <N> — Maximum results (default: 5)

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similar <QUERY>

Find code similar to a query using vector embeddings (cosine similarity).

synapseed similar "error handling" --top-k 5 --min-similarity 0.4

Options:

• --top-k, -k <N> — Number of results (default: 5)
• --min-similarity, -m <FLOAT> — Minimum cosine similarity (default: 0.3)

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architect

Analyze project structural health: score, coupling, cycles, violations.

synapseed architect --refresh

Options:

• --refresh — Force fresh analysis (skip cache)

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consult <QUERY>

Consult the project's architecture policy (DNA config).

synapseed consult "what libraries should I use for HTTP?"

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janitor

Run the Janitor: scan for clippy warnings and unused dependencies.

synapseed janitor

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verify <PATH>

Verify whether a file path exists in the project. Prevents LLM hallucination.

synapseed verify src/main.rs
# { "exists": true, "size_bytes": 1234, "language": "Rust", "is_file": true }

synapseed verify nonexistent.rs
# { "exists": false }

Path traversal attempts (e.g., ../../../etc/passwd) are blocked.

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train <SOURCE>

Evaluate Rust code in the Gym sandbox.

synapseed train src/lib.rs --tests tests/eval.rs --fuzz --adversarial

Options:

• --tests, -t <FILE> — Test file path
• --timeout <SECS> — Timeout (default: 60)
• --fuzz — Enable proptest fuzzing
• --adversarial — Enable mutation testing