From 524289fb663f12ed5abb8923d9a933481acfda60 Mon Sep 17 00:00:00 2001
From: nucleusjay <nucleusjay@gmail.com>
Date: Tue, 9 Jun 2026 03:36:19 -0400
Subject: [PATCH] Fix two latent bugs: merge-chunks output and manifest data
 loss

1. graphify merge-chunks dumped the entire node list to the terminal
   instead of the node count. __main__.py concatenated merged['nodes']
   (a list of dicts) into an f-string where it clearly meant
   len(merged['nodes']) -- the other two values in the same line use
   len() correctly.

2. global_graph._load_manifest silently returned a fresh empty manifest
   on any JSON parse error. That is reachable through normal interrupted
   writes (the manifest is rewritten in full on every global_add /
   global_remove, with no fsync or atomic rename), and the failure mode
   is total data loss: every tracked repo disappears from
   ~/.graphify/global-manifest.json on the next read.

   Back the corrupt file up to <path>.corrupt.<unix_ts> and print to
   stderr before returning the empty default. Users can then recover
   manually and the failure is visible rather than silent.
---
 graphify/__main__.py     |  2 +-
 graphify/global_graph.py | 23 +++++++++++++++++++++--
 2 files changed, 22 insertions(+), 3 deletions(-)

diff --git a/graphify/__main__.py b/graphify/__main__.py
index 759d913b..ce6f15e9 100644
--- a/graphify/__main__.py
+++ b/graphify/__main__.py
@@ -4520,7 +4520,7 @@ def main() -> None:
         out_path.parent.mkdir(parents=True, exist_ok=True)
         out_path.write_text(json.dumps(merged, ensure_ascii=False), encoding="utf-8")
         print(
-            f"Merged {len(chunk_files)} chunks: {merged['nodes']} nodes, {len(merged['edges'])} edges, "
+            f"Merged {len(chunk_files)} chunks: {len(merged['nodes'])} nodes, {len(merged['edges'])} edges, "
             f"{merged['input_tokens']:,} in / {merged['output_tokens']:,} out tokens"
         )
 
diff --git a/graphify/global_graph.py b/graphify/global_graph.py
index c6310f94..24e2af27 100644
--- a/graphify/global_graph.py
+++ b/graphify/global_graph.py
@@ -16,8 +16,27 @@ def _load_manifest() -> dict:
     if _GLOBAL_MANIFEST.exists():
         try:
             return json.loads(_GLOBAL_MANIFEST.read_text(encoding="utf-8"))
-        except Exception:
-            pass
+        except Exception as exc:
+            # Don't silently wipe the user's manifest on a parse error: that
+            # deletes every tracked repo. Back the bad file up and surface the
+            # error so the user can recover or report it.
+            backup = _GLOBAL_MANIFEST.with_suffix(
+                _GLOBAL_MANIFEST.suffix + f".corrupt.{int(datetime.now(timezone.utc).timestamp())}"
+            )
+            try:
+                _GLOBAL_MANIFEST.rename(backup)
+                print(
+                    f"[graphify global] manifest at {_GLOBAL_MANIFEST} failed to parse ({exc}); "
+                    f"moved to {backup} and starting fresh. Restore from the backup if this was "
+                    f"unexpected.",
+                    file=sys.stderr,
+                )
+            except Exception as rename_exc:
+                print(
+                    f"[graphify global] manifest at {_GLOBAL_MANIFEST} failed to parse ({exc}) "
+                    f"and could not be backed up ({rename_exc}). Starting fresh.",
+                    file=sys.stderr,
+                )
     return {"version": 1, "repos": {}}