extract: document basename-uniqueness invariant + skip _-prefixed archive files

Two nits from Ganymede review of ed4af4d:

1. Archive-basename filter depends on basename-uniqueness across queue+archive.
   Current naming (date-prefix + topic-slug) makes collisions rare, but if
   short generic names like "notes.md" enter the queue, the filter silently
   false-positives. Comment block names the assumption.

2. Archive walk now skips _-prefixed files, matching the standing convention
   everywhere else (search.py STRUCTURAL_FILES, reweave wiki-link skip, Layer
   0 entity exclusion). Defensive — no _*.md exists under inbox/archive/
   today, but consistent with codebase convention if a future operator drops
   _README.md to document the directory.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

lib/extract.py

@@ -923,6 +923,36 @@ async def extract_cycle(conn, max_workers=None) -> tuple[int, int]:
         except Exception:
             logger.debug("Failed to read source %s", f, exc_info=True)
 
+    # Archive-basename filter: skip queue files whose basename already exists in
+    # inbox/archive/. Research-session commits on agent branches occasionally
+    # re-introduce already-archived queue files when the branch is re-merged,
+    # producing same-source re-extractions every cooldown cycle. The archive
+    # copy is the source of truth — if a file with this basename is in archive,
+    # the source is processed regardless of queue state. Single archive scan
+    # per cycle, cheap (~1k files).
+    #
+    # Assumes basename uniqueness across queue+archive — current naming
+    # convention (date-prefix + topic-slug) makes collisions vanishingly
+    # rare. If short generic names like "notes.md" enter the queue, this
+    # filter silently false-positives.
+    if unprocessed:
+        archive_dir = main / "inbox" / "archive"
+        archived_basenames: set[str] = set()
+        if archive_dir.exists():
+            for af in archive_dir.rglob("*.md"):
+                if af.name.startswith("_"):
+                    continue
+                archived_basenames.add(af.name)
+        if archived_basenames:
+            before = len(unprocessed)
+            unprocessed = [
+                (sp, c, f) for sp, c, f in unprocessed
+                if Path(sp).name not in archived_basenames
+            ]
+            skipped = before - len(unprocessed)
+            if skipped:
+                logger.info("Skipped %d queue source(s) — basename already in inbox/archive/", skipped)
+
     # Don't early-return here — re-extraction sources may exist even when queue is empty
     # (the re-extraction check runs after open-PR filtering below)