Merge origin/staging into bench-combined; resolve conflicts

Conflict resolution (8 files):
- api/llm.py -> OURS (bench): keep the graphrag-sdk 1.x text-to-Cypher
  rewrite. Required for consistency with the merged pyproject pin
  (graphrag-sdk>=1.1.1); staging's llm.py still imports KnowledgeGraph,
  which 1.x removed, so taking staging would ImportError at load.
- api/analyzers/source_analyzer.py, analyzer.py, python/ts_resolver.py,
  api/mcp/tools/structural.py -> STAGING: canonical/superset versions
  (parallel index workers + missing-file guard, refined logging,
  per-match capture alignment + threading lock, impact_analysis limit).
- tests/analyzers/test_ts_python_resolver.py,
  tests/mcp/fixtures/expected.yaml, tests/mcp/test_impact_analysis.py
  -> STAGING: refined fixtures and added regression tests.

Align MCP surface to staging (drop the deliberately-removed `ask` tool):
- Revert api/mcp/tools/__init__.py to structural-only registration.
- Delete api/mcp/tools/ask.py, api/mcp/graphrag_init.py,
  api/mcp/code_prompts.py and their tests. The ask tool was dropped from
  staging via #702 and is broken under graphrag-sdk 1.x (needs the 0.8
  KnowledgeGraph API and api.llm.define_ontology, both gone in the
  bench rewrite).

Tests: tests/mcp + tests/analyzers (79) and bench/swebench suites pass
(bench_runner needs the mini-swe-agent extra, installed in CI).

Co-authored-by: Copilot <223556219+Copilot@users.noreply.github.com>

Author: DvirDukhan

tests/mcp/fixtures/sample_project/.gitignore

@@ -0,0 +1,6 @@
+# Keep the fixture deterministic: jedi/multilspy historically auto-created
+# a venv/ here during indexing, which polluted the tree with hundreds of
+# stdlib + site-packages files and broke the exact-count contract.
+venv/
+__pycache__/
+*.pyc