Add MCP - #689

docs/source/user/agents.rst:124

• The manual-start examples use qdk_chem_mcp, but the script added in this PR is qdkchemmcp (and the CLI help text elsewhere uses qc). This mismatch will confuse users and makes the docs copy/paste-fail unless an alias exists.
  .github/plugin/marketplace.json:15
• The plugin entry version is also set to 2.0.0 here, which conflicts with the plugin manifest version (2.1.0). Align the entry version so marketplace clients report the correct installed version.

      "name": "qdk-chemistry",
      "description": "Run QDK Chemistry workflows with specialized agents, skills, and MCP tools.",
      "version": "2.0.0",
      "source": "copilot-plugins/qdk-chemistry"

Previously missed (3) — in code that hasn't changed since the last review.

.pre-commit-config.yaml:52

• Setting interrogate’s --fail-under to 0 effectively disables docstring coverage enforcement while still running the hook. If the intent is to keep doc coverage meaningful, restore a non-trivial threshold (e.g., the previous 80) or remove the hook entirely.

    args: [--fail-under=0, --verbose, --ignore-init-method]

python/src/qdk_chemistry/ui/io.py:23

• Path stripping uses rsplit("/", ...), which is not portable on Windows paths ("\"). Use os.path.basename to reliably drop directory components across platforms.

This issue also appears in the following locations of the same file:

• line 63
• line 86
  python/src/qdk_chemistry/ui/validation.py:118

• validate_project is a decorator and always returns a callable wrapper, but its type signature/docstring currently suggest it may return a JSON string. The wrapper actually returns a plain error string on validation failure. Updating the annotation and docstring will prevent confusing API/docs for tool authors.

python/src/qdk_chemistry/ui/io.py:86

• Path stripping uses rsplit("/", ...), which is not portable on Windows paths ("\"). Use os.path.basename to reliably drop directory components across platforms.
  python/src/qdk_chemistry/ui/io.py:63
• Path stripping uses rsplit("/", ...), which is not portable on Windows paths ("\"). Use os.path.basename to reliably drop directory components across platforms.

Suppressed comments (2)

python/src/qdk_chemistry/ui/validation.py:226

• validate_project docstring says the wrapper returns a JSON string on failure, but the implementation returns a plain text message (not JSON). This mismatch can confuse callers and documentation readers; either update the docstring or return structured JSON.
  docs/source/conf.py:361
• normalize_public_export_modules() is executed at import-time in conf.py and unconditionally imports qdk_chemistry.algorithms / qdk_chemistry.data. If those imports fail in a docs-only environment (e.g., native extensions not built), the entire docs build will crash. Consider guarding this with an ImportError handler so docs can still build (possibly with reduced API output).

# Sphinx 9 resolves type annotations while initializing extensions, before the
# ``builder-inited`` event. Normalize exports as part of loading this config so
# autodoc and sphinx-autodoc-typehints both see the same public object names.
normalize_public_export_modules()

• Files reviewed: 82/85 changed files
• Comments generated: 1
• Review effort level: Lite

Suppressed comments (1)

Previously missed (1) — in code that hasn't changed since the last review.

python/src/qdk_chemistry/ui/config.py:77

• QDKMCPConfig creates scratch/projects/cache/jobs directories during init (import time). For plugin-launched MCP processes that require bind_workspace first (QDK_REQUIRE_WORKSPACE_BINDING=1), this performs filesystem writes before the workspace is bound, undermining the intended isolation.

• Files reviewed: 82/85 changed files
• Comments generated: 0 new
• Review effort level: Lite

• Files reviewed: 82/85 changed files
• Comments generated: 1
• Review effort level: Lite

Suppressed comments (1)

Previously missed (1) — in code that hasn't changed since the last review.

python/src/qdk_chemistry/ui/mcp.py:173

• In _accept_relaxer_middleware, treating Accept: */* as already satisfying both application/json and text/event-stream prevents the middleware from rewriting the header for wildcard-only clients. The docstring above states wildcard-only Accept headers are a known incompatibility that should be fixed by this middleware, so this logic currently won't help those clients and may still yield 406 responses.

• Files reviewed: 82/85 changed files
• Comments generated: 0 new
• Review effort level: Lite

Suppressed comments (2)

Previously missed (2) — in code that hasn't changed since the last review.

python/src/qdk_chemistry/remote/proxy.py:94

• _job_cache_key() truncates the SHA-256 digest to 16 hex chars (64 bits). Since this key is used to isolate jobs/results by owner, a longer digest would reduce the chance of collisions that could cause cross-owner cache/job confusion in shared caches.
  python/src/qdk_chemistry/remote/worker.py:51
• The owner-scoped job_cache_key fallback uses a SHA-256 digest truncated to 16 hex chars (64 bits). Because this key is used for owner isolation in caches, consider using a longer prefix to further reduce collision risk.

• Files reviewed: 82/85 changed files
• Comments generated: 0 new
• Review effort level: Lite

• Files reviewed: 82/85 changed files
• Comments generated: 0 new
• Review effort level: Lite