Create a new clean-room reimplementation project with the standard directory structure, config file, and audit trail. This sets up the analysis/, implementation/, and verification/ directories with proper separation. Use this at the start of a new clean-room project.

Get the current status of the clean-room project including spec progress, team members, and audit trail integrity. Shows a summary of all specifications by status, team composition, and whether the audit chain is intact.

Create a new behavioral specification for a component of the target software. Uses a structured template to guide the analyst through documenting observable behavior without including implementation details. The spec will be in 'draft' status. Available templates: api-endpoint, file-format, protocol, behavior, data-structure, algorithm.

Read the contents of a specification. Analysts can read any spec. Implementers can only read specs that have been handed off (status: 'handed-off'). Monitors can read any spec for review purposes.

List all specifications in the project. Supports filtering by status. Implementers will only see specs with status 'handed-off'. Returns a summary of each spec with name, status, template, and target component.

Submit a draft specification for contamination review by the monitor. The monitor will check that the spec contains no implementation details, source code, or internal architecture from the original. Only draft or rejected specs can be submitted.

Review a submitted specification for contamination. Check that it contains only observable behavior descriptions and no implementation details from the original software. Approve it for handoff or reject it with specific feedback about which sections need revision.

Release an approved specification to the implementation team. This copies the spec to the handoff directory, makes it available as an MCP Resource for implementer agents, and creates a signed audit record of the handoff. This action is IRREVERSIBLE — once handed off, the spec cannot be modified.

Add a team member (human or AI agent) to the clean-room project. Each member is assigned a role that determines their tool access. Only the lead role can add team members.

List all team members in the clean-room project with their roles, types (human/AI), and any associated metadata.

Record a formal attestation for the clean-room process. For human team members, this confirms they have not accessed restricted materials. For AI agents, this records what data the agent had access to, including training data disclosures. Attestations are permanently recorded in the audit trail.

Log AI agent activity to the audit trail. Call this to record significant actions taken by AI agents, including session starts, model identifiers, and context that was provided to the agent.

View the project's tamper-evident audit trail. Every tool call, spec handoff, review decision, access denial, and attestation is logged with timestamps and hash-chained entries. Supports filtering by type and date.

Verify the integrity of the project's audit trail by checking the SHA-256 hash chain. If any entry has been modified, added, or removed, this will detect the break point. All roles can verify the audit trail.

Export the complete audit trail as JSON or CSV for compliance records and legal documentation. The export includes all entries with their hash chain, timestamps, and actor information.

Read a specification that has been handed off to the implementation team. Returns the full spec content along with extracted acceptance criteria that the implementation must satisfy. Only handed-off specs are accessible through this tool.

Run the test suite for the reimplementation. Executes the test command in the implementation directory and returns results. Optionally filter to tests for a specific spec.

Compare the reimplementation's behavior against the original software using black-box testing. Feeds identical inputs to both commands and compares outputs. Does NOT access or analyze source code of either — both are treated as opaque executables. Comparison modes: exact (byte-for-byte), fuzzy (whitespace-normalized), semantic (JSON-aware).

Generate a report from the most recent verification run, or a summary of all verification runs. Includes match rates, mismatched cases, and spec coverage.