fix(registry-lint): drop duplicate exploratory-on-disk check

Route the CLI through lint_registry() so ARCH-004's on-disk exploratory
check runs once (matching the library aggregator) and cannot drift.

Co-authored-by: Ravindra Kumar <ravidsrk@gmail.com>

Author: cursoragent

CHANGELOG.md

@@ -65,7 +65,7 @@ surface, an instruction-budget diet, and a pruned mission catalog.
   single-agent-first critique, documents `fleet-verify`, and fixes the dead Orca link
   (`diggerhq/orca` → `stablyai/orca`).
 - Architecture/menu counts, plugin description, and guide/docs-site catalog updated to
-  12 exploratory + 6 archived; test suite now 73 files / 1585 tests.
+  12 exploratory + 6 archived; test suite now 73 files / 1586 tests.
 
 ### Removed
 

README.md

@@ -391,7 +391,7 @@ Individual validators:
 ./scripts/validate-fleet-outcome.sh                # readiness doc fleet-outcome YAML
 ./scripts/validate-goal-condition.sh --scan-docs   # /goal binding
 python scripts/validate_run_archive.py             # Layers 3 & 4: manifest + sha256 + mtime ordering (the blind-fix anti-anchoring ordering IS Layer 3)
-pytest tests/                                      # full suite (73 files, 1585 tests; 100% line coverage of the Python tooling, scripts/*.py — shell is validated by behavioral + mutation tests, not line coverage)
+pytest tests/                                      # full suite (73 files, 1586 tests; 100% line coverage of the Python tooling, scripts/*.py — shell is validated by behavioral + mutation tests, not line coverage)
 
 # Operator gates (run on a specific run-id)
 python scripts/verify_findings.py \
@@ -497,7 +497,7 @@ autonomous-fleet/
 │   ├── lib/                             # fleet_outcome, fleet_run, verify_findings, verify_blind_fix, emit_trace, analyze_seat, analyze_cost, locks, substrate_disable, stop_verify, mission_registry, venv-bootstrap
 │   └── install-skills.sh
 ├── action.yml                           # GitHub Action: fleet-verify as a PR-side gate
-├── tests/                               # 73 test files, 1585 tests; validators + engine doctrine + 4-layer substrate
+├── tests/                               # 73 test files, 1586 tests; validators + engine doctrine + 4-layer substrate
 ├── .agents/skills/                      # installed skill copies (gitignored)
 └── skills-lock.json                     # lockfile for npx skills
 ```

scripts/registry_lint.py

@@ -29,19 +29,9 @@ def main() -> int:
             return 1
         return announce_disabled("registry-lint", "FLEET_DISABLE_REGISTRY_LINT")
     root = Path(sys.argv[1]) if len(sys.argv) > 1 else Path(".")
-    errors = (
-        rl.lint_shipped_mission_dirs(root)
-        + rl.lint_catalog_mentions(root)
-        + rl.lint_skills_lock(root)
-        + rl.lint_lock_hashes(root)
-        + rl.lint_no_skill_version_literals_in_tests(root)
-        + rl.lint_mission_state_docs(root)
-        + rl.lint_adapter_contract_single_source(root)
-        + rl.lint_external_source_pins(root)
-        + rl.lint_campaign_missions(root)
-        + rl.lint_exploratory_on_disk_registered(root)
-        + rl.lint_exploratory_on_disk_registered(root)
-    )
+    # Delegate to the library aggregator so CLI and lint_registry() never drift
+    # (ARCH-004: exploratory-on-disk check must appear exactly once).
+    errors = rl.lint_registry(root)
     for e in errors:
         print(f"registry-lint: {e}", file=sys.stderr)
     return 1 if errors else 0

tests/test_registry_lint_cli.py

@@ -255,3 +255,20 @@ def test_exploratory_on_disk_registered_flags_orphan_and_skips_archive(tmp_path:
 def test_exploratory_on_disk_registered_empty_when_base_missing(tmp_path: Path):
     assert rl.lint_exploratory_on_disk_registered(tmp_path, missions={}) == []
 
+
+def test_cli_does_not_duplicate_exploratory_on_disk_errors(tmp_path: Path):
+    """Greptile #148: CLI must call lint_exploratory_on_disk_registered once.
+
+    An unregistered exploratory mission should emit exactly one registry-lint
+    line for that slug — not a duplicated pair from a double append.
+    """
+    base = tmp_path / "docs" / "exploratory" / "missions" / "orphan-mission"
+    base.mkdir(parents=True)
+    (base / "SKILL.md").write_text("# orphan\n", encoding="utf-8")
+    # Minimal skills/ so other lints don't drown the assertion; empty root still
+    # produces many shipped-dir errors, so filter to the exploratory message.
+    rc, _out, err = _run_cli(str(tmp_path))
+    assert rc == 1
+    hits = [line for line in err.splitlines() if "orphan-mission" in line]
+    assert len(hits) == 1, f"expected one orphan-mission error, got {hits!r}"
+