fix: wire crx_refined into pipeline, fix hardcoded min_coverage

- Add --crx-method (standard|refined) to CLI and analyze_directory
- Pass crx_method through analyze_by_package → _infer_group
- Fix hardcoded min_coverage=0.2 in 3 places (was ignoring parameter)
- Refined CRX wraps crx_with_confidence into standard result format

bex/tag_preprocessor/analyze.py

@@ -256,7 +256,7 @@ def analyze_clusters(file_paths, extension, project_root="", min_coverage=DEFAUL
     if not sequences:
         return []
 
-    sequences = frequency_filter(sequences, min_coverage=0.2)
+    sequences = frequency_filter(sequences, min_coverage=min_coverage)
 
     cluster_fps = set(seq_files)
     imports = _extract_imports(cluster_fps)
@@ -282,9 +282,9 @@ def analyze_clusters(file_paths, extension, project_root="", min_coverage=DEFAUL
     return [("(all methods)", result, len(sequences), meta)]
 
 
-def _infer_group(label, group_seqs, group_files, project_root, min_coverage, prefer, kmax, N, include_kore=False, method='langsize', min_methods=5):
+def _infer_group(label, group_seqs, group_files, project_root, min_coverage, prefer, kmax, N, include_kore=False, method='langsize', min_methods=5, crx_method='standard'):
     """Infer grammar for one package group. Module-level for ProcessPoolExecutor."""
-    filtered = frequency_filter(group_seqs, min_coverage=0.2)
+    filtered = frequency_filter(group_seqs, min_coverage=min_coverage)
     imports = _extract_imports(group_files)
     arg_patterns = _build_arg_patterns(group_files)
     packages = _top_packages(group_files, project_root)
@@ -302,12 +302,21 @@ def _infer_group(label, group_seqs, group_files, project_root, min_coverage, pre
         meta = {"files": group_files, "imports": imports, "arg_patterns": arg_patterns, "packages": packages, "skip_reason": "too_diverse"}
         return (label, None, len(filtered), meta)
 
+    if crx_method == 'refined':
+        from ..crx_refined import crx_with_confidence
+        info = crx_with_confidence(symbol_seqs)
+        result = {
+            'best': {'algorithm': 'CRX-refined', 'grammar': info['grammar'], 'mdl_score': info['confidence']},
+            'all': [{'algorithm': 'CRX-refined', 'grammar': info['grammar'], 'mdl_score': info['confidence']}],
+            'why': f"CRX-refined (confidence={info['confidence']:.2f})",
+        }
+    else:
         result = infer_ensemble(symbol_seqs, kmax=kmax, N=N, prefer=prefer, min_coverage=min_coverage, include_kore=include_kore)
     meta = {"files": group_files, "imports": imports, "arg_patterns": arg_patterns, "packages": packages}
     return (label, result, len(filtered), meta)
 
 
-def analyze_by_package(file_paths, extension, project_root="", min_coverage=DEFAULT_COVERAGE, prefer=None, kmax=2, N=3, min_pkg_size=3, include_kore=False, method='langsize', min_methods=5):
+def analyze_by_package(file_paths, extension, project_root="", min_coverage=DEFAULT_COVERAGE, prefer=None, kmax=2, N=3, min_pkg_size=3, include_kore=False, method='langsize', min_methods=5, crx_method='standard'):
     """Preprocess and group by package directory, infer per group.
 
     Groups methods by their file's relative directory path, merging
@@ -342,7 +351,7 @@ def analyze_by_package(file_paths, extension, project_root="", min_coverage=DEFA
             gs = [sequences[i] for i in indices]
             gf = set(seq_files[i] for i in indices)
             f = ex.submit(_infer_group, label, gs, gf, project_root,
-                           min_coverage, prefer, kmax, N, include_kore, method, min_methods)
+                           min_coverage, prefer, kmax, N, include_kore, method, min_methods, crx_method)
             futures[f] = label
 
         for f in as_completed(futures):
@@ -375,7 +384,7 @@ def infer(file_paths, extension, min_coverage=DEFAULT_COVERAGE, prefer=None, kma
         Ensemble result dict from infer_ensemble.
     """
     sequences, _ = _preprocess_files(file_paths)
-    sequences = frequency_filter(sequences, min_coverage=0.2)
+    sequences = frequency_filter(sequences, min_coverage=min_coverage)
 
     symbol_seqs = [[text for _, text, _ in seq] for seq in sequences]
 
@@ -453,6 +462,7 @@ def analyze_directory(
     include_kore=False,
     method='langsize',
     min_methods=5,
+    crx_method='standard',
 ):
     """Scan a directory and run analysis for each language found.
 
@@ -489,6 +499,7 @@ def analyze_directory(
                 include_kore=include_kore,
                 method=method,
                 min_methods=min_methods,
+                crx_method=crx_method,
             )
         else:
             results[ext] = analyze_clusters(
@@ -650,6 +661,10 @@ def _parse_args(argv=None):
         "--min-methods", type=int, default=5,
         help="Minimum methods per group to infer grammar (default: 5). Groups with fewer are skipped.",
     )
+    parser.add_argument(
+        "--crx-method", choices=["standard", "refined"], default="standard",
+        help="CRX method: standard (default) or refined (cluster-then-infer, tighter grammars)",
+    )
     return parser.parse_args(argv)
 
 
@@ -671,6 +686,7 @@ def main():
         include_kore=args.kore,
         method=args.scoring_method,
         min_methods=args.min_methods,
+        crx_method=args.crx_method,
     )
 
     if args.json_flag or args.format == "json":