fix(bootstrap): improve logging and graph cleanup

1. **Fix logging condition for multiple-versions mode**
   - Change from `if len(results) > 1` to `if self.multiple_versions`
   - Now logs version count whenever multiple-versions mode is requested,
     not just when we get more than 1 result
   - Helps users understand what happened even when 0 or 1 versions match
   - Applied in both resolve_and_add_top_level() and bootstrap()

2. **Fix dangling parent references in dependency graph**
   - Problem: remove_dependency() only cleaned up forward edges (children)
     but not back-references (parents), leaving dangling references
   - Solution: Before deleting node, iterate children and remove the
     back-references from each child's parents list
   - Prevents issues in graph traversals like _collect_dependents()
   - Updated docstring to document both cleanup operations

All 447 unit tests pass. All graph-related e2e tests pass.

Co-Authored-By: Claude Sonnet 4.5 <noreply@anthropic.com>
Signed-off-by: Rohan Devasthale <rdevasth@redhat.com>

Author: rd4398

src/fromager/bootstrapper.py

@@ -162,7 +162,7 @@ def resolve_and_add_top_level(
                 req_type=RequirementType.TOP_LEVEL,
                 return_all_versions=self.multiple_versions,
             )
-            if len(results) > 1:
+            if self.multiple_versions:
                 logger.info(f"resolved {len(results)} version(s) for {req}")
 
             # Add all resolved versions to the graph
@@ -289,7 +289,7 @@ def bootstrap(self, req: Requirement, req_type: RequirementType) -> None:
                 req_type=req_type,
                 return_all_versions=self.multiple_versions,
             )
-            if len(resolved_versions) > 1:
+            if self.multiple_versions:
                 logger.info(f"resolved {len(resolved_versions)} version(s) for {req}")
         except Exception as err:
             if not self.test_mode:

src/fromager/dependency_graph.py

@@ -343,7 +343,9 @@ def remove_dependency(
     ) -> None:
         """Remove a dependency node from the graph.
 
-        Removes the node and all edges pointing to it from parent nodes.
+        Removes the node and all edges pointing to it. This includes:
+        - Back-references in child nodes' parents lists
+        - Forward edges in parent nodes' children lists
         Child nodes of the removed node are kept if referenced elsewhere.
 
         Args:
@@ -357,11 +359,21 @@ def remove_dependency(
 
         logger.debug(f"Removing failed dependency {key} from graph")
 
+        deleted_node = self.nodes[key]
+
+        # Clean up back-references (parents) in nodes that were children of the removed node
+        for child_edge in deleted_node.children:
+            child_node = child_edge.destination_node
+            filtered_parents = [
+                edge for edge in child_node.parents if edge.destination_node.key != key
+            ]
+            child_node.parents.clear()
+            child_node.parents.extend(filtered_parents)
+
         # Remove the node itself
         del self.nodes[key]
 
-        # Remove all edges pointing to this node from parent nodes
-        # Use list comprehension to filter, then clear and re-add
+        # Remove forward edges from any node whose children pointed to the removed node
         for node in self.nodes.values():
             filtered_children = [
                 edge for edge in node.children if edge.destination_node.key != key