fix(merge): preserve repository-local identities

[oleksii-tumanov]

Summary

• keep node IDs, hyperedges and existing community partitions distinct for each repository in merge-graphs
• derive deterministic repository tags from input paths, including configured graph output dirs, and allow one explicit --repo-tag per input
• carry forward valid repository-local hyperedges while pruning malformed entries or unknown members
• leave persistent global add updates for a follow-up after this merge behavior is reviewed

Related to #585

Result

Relevant excerpt from the same orders and payments inputs (community and hyperedge fields condensed):

Before (v8)

Merged 2 graphs -> 4 nodes, 2 edges
orders communities: 0, 1
payments communities: 0, 1
hyperedges: []

Community IDs overlap, and both hyperedges are dropped.

After

Merged 2 graphs [orders, payments] -> 4 nodes, 2 edges, 2 hyperedges
orders communities: 0, 1
payments communities: 2, 3
orders::request_flow -> [orders::entry, orders::worker]
payments::request_flow -> [payments::entry, payments::worker]

Communities are disjoint and both repository-local hyperedges survive.

Testing

• uv run --frozen pytest tests/test_merge_graphs_cli.py -q (12 passed)
• uv run --frozen pytest tests/test_merge_graphs_cli.py tests/test_global_graph.py tests/test_hypergraph.py tests/test_build_merge_hyperedges_and_prune.py tests/test_export.py -q (98 passed)
• uv run --frozen ruff check graphify/build.py graphify/cli.py tests/test_merge_graphs_cli.py (passed)
• uv run --frozen graphify update . (rebuilt graph.json and GRAPH_REPORT.md; no tracked changes)

[oleksii-tumanov]

Rebased after the module-layout changes from #1737 and re-ran the repo guidance check:

• uv run --frozen graphify update . rebuilt graph.json and GRAPH_REPORT.md; no tracked changes remained.