Fix: RemapCollisions deletes existing issue dependencies (GH #120, bd-56)

Bug: updateDependencyReferences() was incorrectly updating ALL dependencies
in the database during collision resolution with --resolve-collisions,
including dependencies belonging to existing issues.

Root cause: The function checked if dep.IssueID was in idMapping keys
(old imported IDs like 'bd-1'), but those are also the IDs of existing
database issues. This caused existing dependencies to be incorrectly
modified or deleted.

Fix: Changed logic to only update dependencies where IssueID is in
idMapping VALUES (new remapped IDs like 'bd-295'). This ensures only
dependencies from remapped issues are updated, not existing ones.

During normal import flow, this is effectively a no-op since imported
dependencies haven't been added to the database yet when RemapCollisions
runs (they're added later in Phase 5 of import_shared.go).

Changes:
- Updated updateDependencyReferences() in collision.go to build a set
  of new remapped IDs and only update dependencies with those IDs
- Added comprehensive documentation explaining the correct semantics
- Added regression tests: TestRemapCollisionsRemapsImportedNotExisting
  and TestRemapCollisionsDoesNotUpdateNonexistentDependencies
- Skipped 3 tests that expected the old buggy behavior with clear
  notes about why they need to be rewritten

Real-world impact: In one case, 125 dependencies were incorrectly
deleted from 157 existing issues during collision resolution.

Fixes https://github.com/steveyegge/beads/issues/120
Fixes bd-56

internal/storage/sqlite/collision_test.go

@@ -894,7 +894,12 @@ func TestRemapCollisions(t *testing.T) {
 	}
 }
 
+// SKIPPED: This test expects the OLD buggy behavior where existing issue dependencies
+// get updated during collision resolution. Per GH issue #120, existing dependencies
+// should be preserved, not updated. This test needs to be rewritten to test the correct
+// semantics (only update dependencies belonging to remapped issues, not existing ones).
 func TestUpdateDependencyReferences(t *testing.T) {
+	t.Skip("Test expects old buggy behavior - needs rewrite for GH#120 fix")
 	// Create temporary database
 	tmpDir, err := os.MkdirTemp("", "dep-remap-test-*")
 	if err != nil {