fix: Ganymede review — explicit staging, push after commit, challenged_by reciprocal

Three fixes from Ganymede's review of extract-time-connection:
1. Replace git add -A with explicit file staging in _reciprocal_edges
2. Push to origin/main immediately after commit (survive batch-extract reset)
3. RECIPROCAL_EDGE_MAP: challenges→challenged_by (not symmetric)
   Added challenged_by to REWEAVE_EDGE_FIELDS, EDGE_FIELDS, EDGE_WEIGHTS

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

lib/merge.py

@@ -390,7 +390,16 @@ async def _cherry_pick_onto_main(branch: str) -> tuple[bool, str]:
         await _git("branch", "-D", clean_branch)
 
 
-REWEAVE_EDGE_FIELDS = ("supports", "challenges", "depends_on", "related", "reweave_edges")
+REWEAVE_EDGE_FIELDS = ("supports", "challenges", "challenged_by", "depends_on", "related", "reweave_edges")
+
+# When A supports B, B also supports A (approximately symmetric).
+# When A challenges B, B is challenged_by A (NOT symmetric — direction matters).
+RECIPROCAL_EDGE_MAP = {
+    "supports": "supports",
+    "challenges": "challenged_by",
+    "related": "related",
+    "depends_on": "related",  # A depends_on B → B is related to A (not symmetric)
+}
 
 
 def _parse_yaml_frontmatter(text: str) -> tuple[dict | None, str, str]:
@@ -1143,6 +1152,7 @@ async def _reciprocal_edges(main_sha: str, branch_sha: str):
             return
 
         reciprocals_added = 0
+        modified_files = set()
         for claim_path in new_claims:
             full_path = config.MAIN_WORKTREE / claim_path
             if not full_path.exists():
@@ -1179,18 +1189,31 @@ async def _reciprocal_edges(main_sha: str, branch_sha: str):
                         continue
 
                     # Add reciprocal edge: target now has field: [new_claim_slug]
-                    if _add_edge_to_file(target_file, field, claim_slug):
+                    reciprocal_type = RECIPROCAL_EDGE_MAP.get(field, "related")
+                    if _add_edge_to_file(target_file, reciprocal_type, claim_slug):
                         reciprocals_added += 1
+                        modified_files.add(str(target_file))
 
         if reciprocals_added > 0:
-            # Commit the reciprocal edges
-            await _git("add", "-A", cwd=str(config.MAIN_WORKTREE))
+            # Stage only the files we modified (never git add -A in automation)
+            for f in modified_files:
+                await _git("add", f, cwd=str(config.MAIN_WORKTREE))
             rc, out = await _git(
                 "commit", "-m", f"reciprocal edges: {reciprocals_added} edges from {len(new_claims)} new claims",
                 cwd=str(config.MAIN_WORKTREE),
             )
             if rc == 0:
-                logger.info("reciprocal_edges: %d edges added across %d new claims", reciprocals_added, len(new_claims))
+                # Push immediately — batch-extract-50.sh does reset --hard origin/main
+                # every 15 min, which destroys unpushed local commits
+                push_rc, push_out = await _git(
+                    "push", "origin", "main",
+                    cwd=str(config.MAIN_WORKTREE),
+                    timeout=30,
+                )
+                if push_rc == 0:
+                    logger.info("reciprocal_edges: %d edges pushed to main (%d new claims)", reciprocals_added, len(new_claims))
+                else:
+                    logger.warning("reciprocal_edges: push failed (commit is local only): %s", push_out[:200])
             else:
                 logger.warning("reciprocal_edges: commit failed: %s", out[:200])
 

lib/search.py

@@ -236,6 +236,7 @@ def graph_expand(seed_paths: list[str], repo_root: Path | None = None,
     """
     EDGE_WEIGHTS = {
         "challenges": 1.5,
+        "challenged_by": 1.5,
         "depends_on": 1.25,
         "supports": 1.0,
         "related": 1.0,

reweave.py

@@ -46,7 +46,7 @@ QDRANT_COLLECTION = os.environ.get("QDRANT_COLLECTION", "teleo-claims")
 FORGEJO_URL = os.environ.get("FORGEJO_URL", "http://localhost:3000")
 
 EMBED_DIRS = ["domains", "core", "foundations", "decisions", "entities"]
-EDGE_FIELDS = ("supports", "challenges", "depends_on", "related")
+EDGE_FIELDS = ("supports", "challenges", "challenged_by", "depends_on", "related")
 WIKI_LINK_RE = re.compile(r"\[\[([^\]]+)\]\]")
 
 # Thresholds (from calibration data — Mar 28)