chore: rescue merged stacked PRs #1150 and #1157 into develop

#1148, #1150, and #1157 were reviewed and merged on GitHub, but the two
stacked children landed on their parent feature branches (now stale)
rather than on develop. Only #1148's commits reached develop via the
direct merge. Release PR #1159 (develop → main for v3.3.3) is therefore
missing the LLM refinement, Claude-conversation scanner, and miner-
registry wire-up that were ostensibly part of the release.

This merge brings the stale `feat/llm-entity-refine` branch (which
contains the rolled-up merge commit for #1157 → #1150 → everything
below) into develop so the release tag includes it.

No code changes here — only history recovery.

tests/test_project_scanner.py

@@ -5,6 +5,7 @@ import os
 import shutil
 import subprocess
 from pathlib import Path
+from types import SimpleNamespace
 
 import pytest
 
@@ -480,6 +481,49 @@ def test_discover_entities_prefers_real_signal_over_prose(tmp_path):
     assert "realproj" in proj_names
 
 
+def test_discover_entities_keeps_uncertain_for_llm_when_real_signal(tmp_path):
+    """With --llm, regex-uncertain prose candidates should reach refinement."""
+    (tmp_path / "package.json").write_text(json.dumps({"name": "realproj"}))
+    _init_git_repo(tmp_path)
+    (tmp_path / "doc.md").write_text("Noise appeared. Noise repeated. Noise again.")
+
+    class FakeProvider:
+        def __init__(self):
+            self.prompts = []
+
+        def classify(self, _system, user, json_mode=True):
+            self.prompts.append(user)
+            return SimpleNamespace(
+                text='{"classifications": [{"name": "Noise", "label": "COMMON_WORD"}]}'
+            )
+
+    provider = FakeProvider()
+    d = discover_entities(str(tmp_path), llm_provider=provider, show_progress=False)
+
+    assert len(provider.prompts) == 1
+    assert "Noise" in provider.prompts[0]
+    assert "Noise" not in [e["name"] for cat in d.values() for e in cat]
+
+
+def test_discover_entities_keeps_llm_only_project_uncertain_when_real_signal(tmp_path):
+    """Repo roots should not auto-promote LLM-only tools/topics into projects."""
+    (tmp_path / "package.json").write_text(json.dumps({"name": "realproj"}))
+    _init_git_repo(tmp_path)
+    (tmp_path / "doc.md").write_text("Terraform shipped. Terraform changed. Terraform runs.")
+
+    class FakeProvider:
+        def classify(self, _system, _user, json_mode=True):
+            return SimpleNamespace(
+                text='{"classifications": [{"name": "Terraform", "label": "PROJECT"}]}'
+            )
+
+    d = discover_entities(str(tmp_path), llm_provider=FakeProvider(), show_progress=False)
+
+    assert "realproj" in [e["name"] for e in d["projects"]]
+    assert "Terraform" not in [e["name"] for e in d["projects"]]
+    assert "Terraform" in [e["name"] for e in d["uncertain"]]
+
+
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