feat(cli): expose application commands over MCP - #690

Summary

MCP clients can currently run scans but must switch to the CLI for the rest of the security workflow. This adds application workflow commands to the same MCP server, so agents can inspect saved scans, import and triage findings, validate or patch them, export results, and publish findings.

Stacked on #682. This PR targets dev/kyleb/mcp-scans and incorporates the updated #682 branch after its merge from main.

Changes

• Expose 20 additional tools, for 22 total: component and bulk scans; scan history, rerun, matching and comparison; finding history and triage; GitHub import; export; validation; fix verification; patching; publication checks and publication; hook installation; login status and logout.
• Derive typed inputs from the public CLI manifest. New tools accept args, options, and optional workingDirectory; command group names use underscores. Existing scan and info inputs stay unchanged. No CLI commands, flags, environment variables, or defaults change.
• Run each new tool through the existing CLI in a separate process, retaining its environment, credentials, exit status, structured results or raw output, and stderr diagnostics. Cancellation and disconnects wait for CLI subprocess cleanup; artifacts are retained.
• Keep browser/device sign-in, credential entry, shell completions, MCP/skills installation helpers, and the newer serve and dedupe commands as local CLI actions. Preserve the existing 22-tool MCP scope during the merge and expose only Linear publication, without custom-publication-only inputs.
• Document tool names, examples, side effects, noninteractive inputs, and CLI positional argument limitations. Extend installed-package smoke coverage and package contents validation, with the hook fixture isolated from global Git hooks configuration.
• Add Git to the Docker package-validation stage, which already includes Python on main, so the MCP smoke tests run in the minimal build image. Runtime requirements are unchanged.

Testing

• 244 focused CLI, MCP, mock-scan, and authentication tests passed with zero failures. Discovery still exposes exactly 22 MCP tools; publication tests reject custom-only options.
• Generated-model consistency, MCP and SDK TypeScript checks, package formatting, and git diff --check: passed.
• Portable plugin Ruff checks and source compatibility checks: passed.
• Production build and complete packed/installed npm package validation passed with 402 archive entries and 122 bundled plugin files, including MCP scan preflight, history, CSV export parity, publication dry-run, hook installation, native Node lifecycle/terminal contracts, dashboard assets, and the nested worker.
• Three independent native reviews and independent verification of the exact merge commit: passed.

Tests use isolated synthetic fixtures; no billable scans, changes to existing credentials, or external issue publication were performed.

Risk and rollout

#682 must merge first; this PR can then be retargeted to main. Neither PR is merged by this change.

The new tools have the same local filesystem and credential access as the CLI. Some commands can make billable model calls, modify files or stored findings, remove stored sign-in, or publish external issues and pull requests; tool annotations and server instructions describe those effects. Cancellation stops work but does not roll back completed side effects. Authentication setup remains outside MCP, and commands that normally offer terminal pickers need explicit inputs.

Public disclosure review

• No customer, partner, prospect, or user identities, data, or identifying details are included.
• No credentials, personal data, private source, scan findings, or nonpublic links or tickets are included.
• I reviewed the branch name, title, description, commits, changes, comments, logs, screenshots, attachments, and links for public disclosure.