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.go

@@ -472,7 +472,21 @@ func replaceIDReferences(text string, idMapping map[string]string) string {
 
 // updateDependencyReferences updates dependency records to use new IDs
 // This handles both IssueID and DependsOnID fields
+// IMPORTANT: Only updates dependencies belonging to REMAPPED issues (with new IDs from idMapping).
+// Dependencies belonging to existing issues are left untouched.
+//
+// NOTE: During normal import flow, this is effectively a no-op because imported dependencies
+// haven't been added to the database yet when RemapCollisions runs. Dependencies are imported
+// later in Phase 5 of import_shared.go. However, this function still serves as a safety guard
+// and handles edge cases where dependencies might exist with the new remapped IDs.
 func updateDependencyReferences(ctx context.Context, s *SQLiteStorage, idMapping map[string]string) error {
+	// Build set of NEW remapped IDs (idMapping values)
+	// Only dependencies with these IDs as IssueID should be updated
+	newRemappedIDs := make(map[string]bool)
+	for _, newID := range idMapping {
+		newRemappedIDs[newID] = true
+	}
+
 	// Get all dependency records
 	allDeps, err := s.GetAllDependencyRecords(ctx)
 	if err != nil {
@@ -489,6 +503,17 @@ func updateDependencyReferences(ctx context.Context, s *SQLiteStorage, idMapping
 
 	for _, deps := range allDeps {
 		for _, dep := range deps {
+			// CRITICAL FIX: Only update dependencies that belong to REMAPPED issues
+			// A dependency belongs to a remapped issue if its IssueID is a NEW remapped ID
+			// (one of the VALUES in idMapping, not the keys)
+			//
+			// We must NOT check against idMapping keys (old IDs) because those are the same
+			// as existing issue IDs in the database, and we'd incorrectly modify their dependencies.
+			if !newRemappedIDs[dep.IssueID] {
+				// This dependency does not belong to a remapped issue - skip it
+				continue
+			}
+
 			needsUpdate := false
 			newIssueID := dep.IssueID
 			newDependsOnID := dep.DependsOnID

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 {