feat: persistent cross-file edge overlays

[chris-asmussen]

Summary

• Adds cross_edges.json support so manually curated or LLM-generated cross-file edges survive AST-only rebuilds (_rebuild_code in watch.py)
• Adds graphify edges CLI with list, add, remove, and prune subcommands for managing cross-file edges
• Includes 13 tests covering rebuild injection, staleness handling, malformed JSON resilience, and all CLI subcommands

Problem

_rebuild_code() preserves semantic nodes/edges where neither endpoint is a code node, but drops cross-file edges between two code nodes. This means community detection produces hundreds of isolated 1-node communities for multi-file codebases in Ruby, TypeScript, Go, etc. where AST extraction can't resolve cross-file calls.

Approach

A persistent graphify-out/cross_edges.json overlay file stores edges that should survive rebuilds. After the existing semantic preservation logic in _rebuild_code(), the new injection block merges these edges into the result dict -- skipping edges where either node no longer exists and deduplicating against edges already present from AST extraction.

The graphify edges CLI provides CRUD operations for managing the overlay without hand-editing JSON.

Complements #315 (global symbol table) -- the symbol table handles statically resolvable calls, while this overlay handles framework conventions (Rails has_many, Django ForeignKey), dynamic dispatch, and user knowledge about architectural intent.

Closes #298

Test plan

• test_preserves_cross_edges -- cross edges with valid nodes are injected
• test_skips_stale_cross_edges -- edges referencing deleted nodes are silently skipped
• test_no_cross_edges_file -- rebuild works identically without cross_edges.json
• test_malformed_cross_edges -- invalid JSON does not crash rebuild
• test_no_duplicate_injection -- existing AST edges are not duplicated
• test_edges_add / test_edges_add_duplicate -- CLI add with dedup
• test_edges_remove / test_edges_remove_not_found -- CLI remove
• test_edges_list_empty / test_edges_list_shows_edges -- CLI list
• test_edges_prune -- removes edges where nodes no longer exist in graph
• test_edges_help -- usage output on missing subcommand