fix(ci): address PR #139 review — 5 issues + source list sync

1. decisions_sync.py: fix refs_created inflation (check rowcount),
   remove dead IntegrityError except block
2. Extract SCHEMA_VERSION to shared tooling/schema_version.py —
   both generators import from single source of truth
3. generate_atlas.py: narrow bare except to OperationalError +
   "duplicate column" check
4. check-systems-db-stamp: add cross-generator schema_version
   agreement assertion (defense-in-depth)
5. decision wrapper: add show + orphan-tickets to usage text
6. Add schema_version.py to all three source watch lists
   (GENERATOR_SOURCES, IMPORT_ECONOMICS_SOURCES, generate_atlas
   _write_stamp) — prevents silent staleness on version bump

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

tooling/db/decision

@@ -1,8 +1,10 @@
 #!/usr/bin/env bash
 # Decision ID management — claim, query, and validate decision IDs.
 # Usage:
-#   decision next [D|Q|R]                Show next available ID
-#   decision claim <D|Q|R> <domain> [title]  Claim next ID (reserves in DB)
-#   decision check-dupes                 Check for duplicate IDs in markdown
-#   decision sync                        Sync markdown -> DB
+#   decision sync                             Sync decisions/*.md into SQLite
+#   decision show <D-NNN>                     Show a decision with linked tickets + refs
+#   decision next [D|Q|R]                     Show next available ID
+#   decision claim <D|Q|R> <domain> [title]   Claim next ID (reserves in DB)
+#   decision check-dupes                      Check for duplicate IDs in markdown
+#   decision orphan-tickets                   List tickets with invalid/missing decision_ref
 exec python3 "$(dirname "$0")/decisions_sync.py" "$@"

tooling/db/decisions_sync.py

@@ -310,16 +310,14 @@ def sync(cfg):
                     )
                     continue
 
-                try:
-                    conn.execute(
-                        """INSERT OR IGNORE INTO decision_refs
-                           (source_id, target_id, ref_type, note)
-                           VALUES (?, ?, ?, ?)""",
-                        (d["id"], target_id, ref_type, note),
-                    )
+                cur = conn.execute(
+                    """INSERT OR IGNORE INTO decision_refs
+                       (source_id, target_id, ref_type, note)
+                       VALUES (?, ?, ?, ?)""",
+                    (d["id"], target_id, ref_type, note),
+                )
+                if cur.rowcount > 0:
                     refs_created += 1
-                except sqlite3.IntegrityError:
-                    pass  # duplicate ref, skip
 
         conn.commit()