Fix consistency reconciliation across deps, workflows, and artifacts

[xpcmdshell]

Summary

• make Session.remove_dep() remove configured packages from the active environment for the in-process, subprocess, and container executors
• refresh persisted workflow reads in long-lived namespaces and the container workflow API so external file changes are observed without restart
• reconcile Redis artifact metadata and file-backed dependency state against their backing store on read
• adjust MCP dep workflow tests to use a leaf package (colorama) for add/remove coverage

What changed

• normalized remove_dep() results across the main executors and updated the container /api/deps/remove endpoint to uninstall as well as update config
• refreshed persisted workflow list/get/search/invoke paths and fixed stale-cache WorkflowLibrary.remove() success reporting
• made RedisArtifactStore prune stale metadata when payload keys are gone
• made FileDepsStore reload requirements.txt on reads and before mutations so external edits stay visible
• hardened cached subprocess venv reuse by validating that ipykernel still imports before reusing an existing env
• updated MCP dep add/list/remove tests to use colorama / colorama>=0.4, which keeps the tests focused on remove_dep() behavior without using a package in the Jupyter kernel dependency chain

Verification

• uv run ruff check src/py_code_mode/deps/store.py src/py_code_mode/execution/in_process/executor.py src/py_code_mode/execution/subprocess/executor.py src/py_code_mode/execution/subprocess/venv.py src/py_code_mode/execution/container/server.py src/py_code_mode/execution/container/client.py src/py_code_mode/execution/container/executor.py src/py_code_mode/execution/in_process/workflows_namespace.py src/py_code_mode/workflows/library.py src/py_code_mode/artifacts/redis.py tests/test_executor_deps_methods.py tests/test_skills_namespace_decoupling.py tests/test_semantic.py tests/container/test_container_api.py tests/test_redis_artifacts.py tests/test_deps_store.py tests/test_deps_installer.py tests/test_subprocess_executor.py
• uv run pytest tests/test_executor_deps_methods.py tests/test_skills_namespace_decoupling.py tests/test_semantic.py tests/container/test_container_api.py tests/test_redis_artifacts.py tests/test_deps_store.py tests/test_deps_installer.py tests/test_subprocess_executor.py
• ./.venv/bin/ruff check tests/test_mcp_server.py
• uv run pytest tests/test_mcp_server.py -k 'add_dep or remove_dep or list_deps' -q
• manual checks outside pytest:
  • FileDepsStore external requirements.txt edit reflected by list() / exists()
  • persisted workflow edit/delete reflected by WorkflowsNamespace.invoke() / search()
  • RedisArtifactStore pruned stale metadata after payload deletion
  • real subprocess session: Session.remove_dep("colorama") removed config, uninstalled from the venv, and after reset import colorama failed with ModuleNotFoundError

Notes

• Deno sandbox removal semantics remain best-effort because Pyodide uninstall is not a true supported uninstall path.
• This PR does not attempt to solve concurrent writer locking/races.
• This PR does not add subprocess dep-protection. Uninstalling kernel-critical packages from a shared cached subprocess env can still break that env; the MCP tests now avoid that sharp edge instead of exercising it.