fix: restore frequency_filter at 0.2, add dual 0.8 BEX coverage

- frequency_filter(min_coverage=0.2) strips rare symbols before clustering/inference
- DEFAULT_COVERAGE=0.8 passed to infer_ensemble for sequence-level core/outlier detection
- Both filters active: symbol-level (0.2) then BEX sequence-level (0.8)
- Fix seq_of_file tracking broken by filter creating new list objects

bex/tag_preprocessor/analyze.py

@@ -155,6 +155,9 @@ def scan_directory(dir_path, gitignore_spec=None):
     return result
 
 
+DEFAULT_COVERAGE = 0.8
+
+
 def frequency_filter(sequences, min_coverage=0.2):
     """Remove symbols appearing in fewer than min_coverage fraction of files.
 
@@ -257,9 +260,12 @@ def cluster_methods_adaptive(sequences, min_cluster_size=3, ngram_size=3, other_
     return clusters
 
 
-def analyze_clusters(file_paths, extension, project_root="", min_coverage=0.2, prefer=None, kmax=2, N=3):
+def analyze_clusters(file_paths, extension, project_root="", min_coverage=DEFAULT_COVERAGE, prefer=None, kmax=2, N=3):
     """Run full pipeline with clustering: preprocess → cluster → per-cluster infer.
 
+    Each cluster gets its own ensemble inference with BEX core/outlier
+    detection at the given min_coverage threshold.
+
     Returns:
         list of (label, ensemble_result_dict, method_count, meta) tuples.
         meta = {"files": set(paths), "imports": [lines], "arg_patterns": {...}, "packages": [...]}.
@@ -277,7 +283,7 @@ def analyze_clusters(file_paths, extension, project_root="", min_coverage=0.2, p
     if not sequences:
         return []
 
-    sequences = frequency_filter(sequences, min_coverage)
+    sequences = frequency_filter(sequences, min_coverage=0.2)
     clusters = cluster_methods_adaptive(sequences)
 
     results = []
@@ -289,7 +295,7 @@ def analyze_clusters(file_paths, extension, project_root="", min_coverage=0.2, p
         imports = _extract_imports(cluster_fps)
         arg_patterns = _build_arg_patterns(cluster_fps)
         symbol_seqs = [[text for _, text, _ in seq] for seq in cluster_seqs]
-        result = infer_ensemble(symbol_seqs, kmax=kmax, N=N, prefer=prefer)
+        result = infer_ensemble(symbol_seqs, kmax=kmax, N=N, prefer=prefer, min_coverage=min_coverage)
         packages = _top_packages(cluster_fps, project_root)
         meta = {"files": cluster_fps, "imports": imports, "arg_patterns": arg_patterns, "packages": packages}
         results.append((label, result, len(cluster_seqs), meta))
@@ -297,13 +303,13 @@ def analyze_clusters(file_paths, extension, project_root="", min_coverage=0.2, p
     return results
 
 
-def infer(file_paths, extension, min_coverage=0.2, prefer=None, kmax=2, N=3):
+def infer(file_paths, extension, min_coverage=DEFAULT_COVERAGE, prefer=None, kmax=2, N=3):
     """Run full pipeline: preprocess → frequency filter → ensemble infer.
 
     Args:
         file_paths: list of source file paths (same language).
         extension: language extension (e.g. '.py').
-        min_coverage: minimum file fraction for a symbol to be kept.
+        min_coverage: BEX core coverage threshold for outlier removal.
         prefer: inference algorithm preference ('crx', 'idregex', or None).
         kmax: max k for k-ORE algorithms.
         N: number of random trials.
@@ -319,16 +325,16 @@ def infer(file_paths, extension, min_coverage=0.2, prefer=None, kmax=2, N=3):
             if method_seq:
                 sequences.append(method_seq)
 
-    sequences = frequency_filter(sequences, min_coverage)
+    sequences = frequency_filter(sequences, min_coverage=0.2)
 
     symbol_seqs = [[text for _, text, _ in seq] for seq in sequences]
 
-    return infer_ensemble(symbol_seqs, kmax=kmax, N=N, prefer=prefer)
+    return infer_ensemble(symbol_seqs, kmax=kmax, N=N, prefer=prefer, min_coverage=min_coverage)
 
 
 def analyze_directory(
     dir_path,
-    min_coverage=0.2,
+    min_coverage=DEFAULT_COVERAGE,
     prefer=None,
     kmax=2,
     include=None,
@@ -410,8 +416,8 @@ def _parse_args(argv=None):
         help="Maximum k for k-ORE algorithms (default: 2)",
     )
     parser.add_argument(
-        "--min-coverage", type=float, default=0.2,
+        "--min-coverage", type=float, default=DEFAULT_COVERAGE,
-        help="Minimum file fraction for a symbol to survive frequency filter (default: 0.2)",
+        help="BEX core coverage threshold — outlier methods are removed until this fraction remains (default: 0.8)",
     )
     parser.add_argument(
         "--include",