USE WHEN: Session lifecycle (orientation, registry, compaction).

EXAMPLES: session(operation="start", goal="Fix auth bug"); session(operation="compact", summary="Session handoff").

Plan lifecycle: create, list, get, complete, register, graph, or archive_completed.

USE WHEN: managing plan files, marking plans complete, registering roadmap entries, or reading the plan dependency graph (operation="graph"). EXAMPLES: plan(operation="create", ...), plan(operation="graph"), plan(operation="register", ...).

Add/remove roadmap entries and append memory-bank entries.

USE WHEN: You need a single memory-bank mutation entrypoint for roadmap edits (add/remove section entries) or append-style updates for progress, active context, or operations log entries.

DO NOT use this tool for free-form markdown rewrites; Prefer targeted operation modes so validation and sync rules remain enforceable.

EXAMPLES:

• update_memory_bank(operation="roadmap_add", section="pending", entry_text="- Improve retrieval scoring")

• update_memory_bank(operation="progress_append", date_str="2026-04-14", entry_text="Implemented typed memory reader")

• update_memory_bank(operation="log_append", operation_type="fix", title="Resolve docs gate mismatch", summary="Aligned roadmap and progress")

Run Phase A quality gate end-to-end and return full result. Zero args required.

USE WHEN: Running the commit pipeline Phase A quality gate or the Step 12 final gate. Spawns checks as a detached subprocess and polls with heartbeat progress notifications, keeping the MCP stdio connection alive.

Config is read from the pipeline session file written by pipeline_handoff(operation="write", pipeline="commit", phase="checks"). Supported keys: coverage_threshold (float), test_timeout (int), force_fresh (bool), reflection (bool), force_reflection (bool). When reflection is enabled and primary checks pass, a heuristic reflection pass runs; error-level findings set preflight_passed to false.

EXAMPLES:

• run_quality_gate() before commit Phase A.

• pipeline_handoff(write, checks, {"force_fresh": true, "test_timeout": 600}) then run_quality_gate() for Step 12 final gate.

Run Phase B docs/memory-bank sync validation. Zero args required.

USE WHEN: Validating that timestamps, roadmap_sync, and memory-bank files are consistent after documentation updates. Called by the commit-docs subagent as a zero-arg alternative to execute_pre_commit_checks(phase="B") (which Cursor's MCP bridge zero-args to Phase A, running tests instead).

RETURNS: JSON with docs_phase_passed (bool), timestamps_result, and roadmap_sync_result. Does NOT run tests or code quality checks.

EXAMPLES:

• run_docs_gate() after updating memory-bank files via manage_file() in Phase B of the commit pipeline.

• run_docs_gate() to re-check roadmap_sync and timestamps without re-running tests or other quality checks.

Auto-fix formatting, linting, type errors, and markdown lint. Zero args required.

USE WHEN: Phase A fails and automated fixes are needed before re-running checks. Called by commit-checks, commit-final-gate, and implement-code agents after preflight_passed=false. Runs fix_errors, format, type_check, and markdown auto-fix.

INTEGRITY SAFEGUARDS:

• Do not use this tool output as a "done" signal by itself; always re-run run_quality_gate() and validate changed modules still import cleanly.

• If a fix iteration introduces new failures/regressions, roll back that attempt and retry with a different approach (max 3 attempts).

EXAMPLES:

• autofix() immediately after a failing run_quality_gate() call to auto-fix formatting, linting, type, and markdown issues.

• autofix() inside implement-code or commit-checks agents on the fix path before re-running the quality gate.

Compress project memory files (CLAUDE.md, .cortex/memory-bank/*.md) to reduce session token cost. Creates .original backups; validates structural integrity before overwriting. Returns per-file compression ratios.

USE WHEN: Attached projects need shorter CLAUDE.md / memory-bank prose after cortex://analysis flags compression candidates, or before long sessions.

DO NOT: Run on source code, tests, or user-facing docs outside memory paths.

EXAMPLES:

• compress_memory_bank() — zero-arg uses MCP workspace root

• compress_memory_bank(project_root="/path/to/project")

RETURNS: JSON with status and result (CompressMemoryBankResult fields).

Inspect or manage the memory-bank WAL (JSONL audit log and snapshots).

USE WHEN: You need an audit trail of memory-bank writes, anomaly hints, or a filesystem snapshot/restore of .cortex/memory-bank/*.md (not a git substitute).

DO NOT: Treat WAL as authoritative security auditing; it is best-effort and can be disabled by disk errors (writes still proceed).

EXAMPLES:

• memory_wal(operation="read") — last 50 WAL entries

• memory_wal(operation="anomalies") — heuristic warnings

• memory_wal(operation="snapshot", label="backup-2026-04-15")

• memory_wal(operation="restore", label="backup-2026-04-15")

Pre-compact automation: there is no bundled Claude PreCompact hook in this repo; run memory_wal(operation="snapshot", label="pre-compact-…") manually before risky compaction if you want a rollback point.

Structured inter-agent communication for pipeline workflows.

USE WHEN: Orchestrators need to exchange structured data between pipeline phases. Each phase writes its output; the next phase reads it. All data persists in .cortex/.session/{id}/{pipeline}/.

WORKFLOW (simplified):

1. pipeline_handoff(operation="init", pipeline="commit")

2. pipeline_handoff(operation="write", pipeline="commit", phase="preflight", data='{"status":"complete","snapshot_ref":"abc123"}')

3. pipeline_handoff(operation="read", pipeline="commit", phase="preflight") → reads phase data

4. pipeline_handoff(operation="read", pipeline="commit") → reads full pipeline state (all phases)

5. pipeline_handoff(operation="clear", pipeline="commit")

EXAMPLES:

• pipeline_handoff(operation="init", pipeline="commit")

• pipeline_handoff(operation="write", pipeline="commit", phase="checks", data='{"status":"passed","coverage":0.94}')

• pipeline_handoff(operation="read", pipeline="commit", phase="checks")

• pipeline_handoff(operation="read", pipeline="commit")

• pipeline_handoff(operation="clear", pipeline="commit")

Legacy aliases (write_task, read_task, write_result, read_state) still work.

RETURNS: JSON with {status, ...} for write ops; JSON file content for reads.

Args: operation: init | write | read | read_log | status | mark_running | clear | snapshot | rollback (legacy: write_task, read_task, write_result, read_state) pipeline: Pipeline name (e.g. "commit", "implement"). Default: "default". phase: Phase name (e.g. "preflight", "checks"). Required for write. For read: if given, reads that phase; if omitted, reads full state. data: Payload for write and init. Accepts JSON string or native object. When the JSON includes free-text fields such as context or summary, write compact technical prose (see cortex://rules, Agent-Internal Communication): no filler or hedging; keep file paths and error messages verbatim. paths: Paths to snapshot for operation="snapshot". Can be passed via this argument or via data={"paths":[...]} for arg-stripping clients. snapshot_id: Snapshot id for operation="rollback". Can be passed via this argument or via data={"snapshot_id":"..."}. ctx: MCP context (auto-provided).

Append a thought to internal scratchpad.

USE WHEN: Agent needs reasoning before action or multi-step deliberation. EXAMPLES: think(thought="Check constraints"), think(thought="Step 1", thought_number=1, total_thoughts=2, next_thought_needed=True).