feat: preserve parallel relations with MultiDiGraph

[hsneves]

Summary

Adds an opt-in --multigraph build mode backed by a directed MultiDiGraph. Canonically distinct relations retain stable keys, exact duplicates aggregate through occurrence_count, and incremental/query/export paths preserve parallel edges without changing the default Graph mode.

Depends on #2174 (8c2af43); this branch is intentionally stacked on that endpoint-materialization fix.

Highlights

• stable keyed parallel edges and exact-duplicate counters
• automatic mode preservation in update/watch/hook/cluster-only/no-cluster
• simple unweighted topology projection for clustering and centrality
• parallel-aware query, path, explain, HTML, wiki, Obsidian, GraphML, graph DB and MCP readers
• explicit failure instead of silent simplification in merge/global flows
• expanded diagnostics for canonical, duplicate, parallel, reciprocal and post-build loss counts
• generated skills document and propagate IS_MULTIGRAPH

Validation

• uv run ruff check .
• uv run python -m tools.skillgen --check (134 artifacts)
• uv run pytest -q: 3598 passed, 33 skipped
• real 698-code/95-semantic-file monorepo: 9,220 nodes, 24,206 canonical edges, 975 distinct parallel instances, 44 reciprocal endpoint pairs, 457 exact duplicate occurrences, 0 unresolved/malformed/unclassified internal endpoints, 0 post-build distinct loss
• StageTrackPaths.__init__ -> Path preserves both references at L982 (occurrence_count=6) and calls at L1002