tools/cube-notes-agent: dedupe findings by ISSUE (not just coord)

_canonical_issue() strips FK/FK#/FA/FB/FLAG/FIX prefixes and normalizes separators so
duplicate representations of one root cause collapse (e.g. FK1-SELINUX_RESTORECON +
SELINUX-RESTORECON -> selinux_restorecon; FK3-WAL_CHECKPOINT +
CONCURRENT-STORE-CHECKPOINT -> checkpoint_before_exit via an alias map). Per issue only
the most-detailed note is reported. mark_covered now covers ALL uncovered finding coords
(including deduped-away duplicates) so nothing re-reports. Corresponding notes re-tagged:
issue logs -> finding, status notes -> impl (no uncategorized notes remain).

tools/cube-notes-agent.py

@@ -160,11 +160,26 @@ def uncovered_findings(project=None):
     un = "".join(f"{coord}  {subj}\n" for coord, cat, subj in _log_findings(project) if coord not in covered)
     return un.strip() or "(no new findings)"
 
+# Canonical issue key: collapse duplicate representations of the same root cause
+# (e.g. FK1-SELINUX_RESTORECON vs SELINUX-RESTORECON) so the report dedupes by ISSUE,
+# not just by coordinate. Prefixes (FK, FK#, FA, FB, FLAG, FIX) are stripped and
+# separators normalized; a small alias map unifies differently-worded duplicates.
+_ISSUE_PREFIX_RE = _re.compile(r'^(FK\d*|FA|FB|FLAG|FIX)[-_]?', _re.I)
+_ISSUE_ALIAS = {
+    "wal_checkpoint": "checkpoint_before_exit",
+    "concurrent_store_checkpoint": "checkpoint_before_exit",
+}
+
+def _canonical_issue(flag):
+    f = _ISSUE_PREFIX_RE.sub('', flag)
+    f = _re.sub(r'[-_/\s]+', '_', f).strip('_').lower()
+    return _ISSUE_ALIAS.get(f, f)
+
 def _uncovered_meta(project=None):
-    """[(coord, flag, desc)] for the currently-UNCOVERED findings (grounded).
-    desc is the FULL note body (not the truncated list subject)."""
+    """[(coord, flag, desc)] for the currently-UNCOVERED findings, DEDUPED BY ISSUE.
+    desc is the FULL note body; the most-detailed note per canonical issue is kept."""
     covered = _covered(project)
-    out = []
+    best = {}   # issue -> (coord, flag, desc, len)
     for coord, cat, subj in _log_findings(project):
         if coord in covered:
             continue
@@ -175,8 +190,11 @@ def _uncovered_meta(project=None):
         flag, sep, rest = body_text.partition(":")
         flag = flag.strip()
         desc = rest.strip() if sep else body_text
-        out.append((coord, flag, desc))
-    return out
+        issue = _canonical_issue(flag)
+        cur = best.get(issue)
+        if cur is None or len(desc) > cur[3]:
+            best[issue] = (coord, flag, desc, len(desc))
+    return [(c, f, d) for c, f, d, _ in best.values()]
 
 # Snapshot of the uncovered findings captured when read_findings ran, so the
 # report can be composed faithfully even after mark_covered has covered them.
@@ -253,10 +271,11 @@ def compose_report(project=None, model_text=""):
     return "\n".join(lines)
 
 def mark_covered(project=None, text=""):
-    meta = CURRENT_META or _uncovered_meta(project)
-    if not meta:
+    covered = _covered(project)
+    coords = [c for c, cat, subj in _log_findings(project) if c not in covered]
+    if not coords:
         return "nothing to cover"
-    body = "covered coords:\n" + "\n".join(f"{coord}  {flag}" for coord, flag, _ in meta)
+    body = "covered coords:\n" + "\n".join(coords)
     args = [CUBE, "note", "add", "--cat", "checkpoint"]
     if project:
         args += ["--project", project]
@@ -368,10 +387,10 @@ def main():
     if not report_text:
         # Run ended without an explicit "done" — still produce a grounded report.
         report_text = compose_report(a.project, last_assistant)
-    if CURRENT_META:
-        # Deterministic coverage: mark the reported findings covered regardless of
-        # whether the model did it, so the next run is genuinely incremental.
-        mark_covered(a.project)
+    # Deterministic coverage: mark all uncovered findings covered (including any
+    # deduped-away duplicates) regardless of whether the model did it, so the next
+    # run is genuinely incremental. No-op when there are no uncovered findings.
+    mark_covered(a.project)
     with open(a.report, "w") as f:
         f.write(report_text)
     os.makedirs(os.path.dirname(a.report), exist_ok=True) if os.path.dirname(a.report) else None