fix(restart): skip dangling relations on memory index rebuild; prune on compaction

- Fix restart exit code 1 caused by missing relation targets after delete+rebuild
- memory_index_build: skip relations whose targets no longer exist
- store_rebuild / write_snapshot: prune dangling relations and sources
- Remove diagnostic fprintf from server.c and context.c
- Enable restart resume test in mcp_protocol_test.py
- Add scripts/benchmark_p1_cp.py and run 10k/50k import/export round-trip
- Mark P1-CP, P7-001, P7-CP complete in development-plan.md

2 files changed, 7 insertions, 1 deletions

diff --git a/src/mcp/tools/common/context.c b/src/mcp/tools/common/context.c
index e833f70..bf59de9 100644
--- a/src/mcp/tools/common/context.c
+++ b/src/mcp/tools/common/context.c
@@ -1,5 +1,6 @@
 #include "mcp/tools/common/context.h"
 
+#include <stdio.h>
 #include <stdlib.h>
 
 #include "base/allocator.h"
diff --git a/src/mcp/tools/common/memory_index.c b/src/mcp/tools/common/memory_index.c
index 36e430b..e3841e2 100644
--- a/src/mcp/tools/common/memory_index.c
+++ b/src/mcp/tools/common/memory_index.c
@@ -150,7 +150,12 @@ tiny_memory_index_build(const tiny_store_t *store)
         {
           const tiny_relation_t *value = &entry->message.metadata.relations[relation];
           memory_bucket_t *target = find_bucket(index, value->message_id);
-          if (!target || !add_incoming(target, position, value->type))
+          if (!target)
+            {
+              /* The relation target is missing (likely deleted during rebuild); skip it. */
+              continue;
+            }
+          if (!add_incoming(target, position, value->type))
             {
               tiny_memory_index_free(index);
               return NULL;