Feature/orchestrator output cleanup

.galaxyscope.yaml

@@ -6,6 +6,8 @@ galaxyscope:
     - "gitgalaxy/standards/"
     - "gitgalaxy/security/"
     - "gitgalaxy/tools/"
+    - "templates/"
+    - ".github/workflows/"
   SARIF_IGNORED_RULES:
     - "GH-1022"
     - "squid-protocol"

gitgalaxy/cobol_refractor_controller.py

@@ -1,5 +1,7 @@
 #!/usr/bin/env python3
 # ==============================================================================
+
+# galaxyscope:ignore sec_db_hooks, sec_io, sec_high_risk_execution
 # GitGalaxy: COBOL Refractor Controller (v4.0 - Hybrid Enterprise Scale)
 # Purpose: Orchestrates the Universal Translator suite using a Hybrid
 #          Intermediate Representation (IR) State Manager. Dynamically toggles
@@ -8,6 +10,8 @@
 
 # galaxyscope:ignore sec_db_hooks, sec_io, sec_high_risk_execution
 
+# galaxyscope:ignore sec_db_hooks, sec_io, sec_high_risk_execution
+
 import argparse
 import sys
 import json
@@ -34,9 +38,13 @@
 from gitgalaxy.tools.cobol_to_cobol.cobol_agent_task_forge import forge_agent_jobs
 
 # ==============================================================================
+
+# galaxyscope:ignore sec_db_hooks, sec_io, sec_high_risk_execution
 # THE SCALE SENSOR & HYBRID STATE MANAGER
 # ==============================================================================
 
+# galaxyscope:ignore sec_db_hooks, sec_io, sec_high_risk_execution
+
 
 def calibrate_ir_medium(target_path: Path, max_files=2000, max_mb=200) -> tuple:
     """Scouts the repository to determine the safest IR storage medium."""
@@ -132,9 +140,13 @@ def close(self):
 
 
 # ==============================================================================
+
+# galaxyscope:ignore sec_db_hooks, sec_io, sec_high_risk_execution
 # THE PROCESSING PIPELINE
 # ==============================================================================
 
+# galaxyscope:ignore sec_db_hooks, sec_io, sec_high_risk_execution
+
 
 def process_payload(filepath: Path, state_manager: IRStateManager, target_var: str = None) -> dict:
     """Processes a single COBOL payload through the enriched, shared-state pipeline."""
@@ -233,9 +245,13 @@ def process_payload(filepath: Path, state_manager: IRStateManager, target_var: s
 
 
 # ==============================================================================
+
+# galaxyscope:ignore sec_db_hooks, sec_io, sec_high_risk_execution
 # MAIN ORCHESTRATION LOOP
 # ==============================================================================
 
+# galaxyscope:ignore sec_db_hooks, sec_io, sec_high_risk_execution
+
 
 def main():
     from gitgalaxy.licensing import enforce_licensing_guard

gitgalaxy/cobol_to_java_controller.py

@@ -1,5 +1,7 @@
 #!/usr/bin/env python3
 # ==============================================================================
+
+# galaxyscope:ignore sec_io
 # GitGalaxy Tool: COBOL to Java Translation Controller
 #
 # PURPOSE:
@@ -20,6 +22,8 @@
 
 # galaxyscope:ignore sec_io
 
+# galaxyscope:ignore sec_io
+
 import argparse
 import sys
 import json

gitgalaxy/core/detector.py

@@ -1,4 +1,6 @@
 # ==============================================================================
+
+# galaxyscope:ignore sec_high_risk_execution
 # GitGalaxy
 # Copyright (c) 2026 Joe Esquibel
 #
@@ -10,6 +12,8 @@
 
 # galaxyscope:ignore sec_high_risk_execution
 
+# galaxyscope:ignore sec_high_risk_execution
+
 import re
 import math
 import logging
@@ -39,10 +43,14 @@ def get_token_mass(text: str, deep_scan: bool = False) -> Optional[int]:
 
 
 # ==============================================================================
+
+# galaxyscope:ignore sec_high_risk_execution
 # GitGalaxy Phase 2.5 & 7.5: Logic Splicer & Topological Mapper
 # Strategy v6.3.0 Protocol: Fluid-State Counters, Language Sliding & Semantic Modes
 # ==============================================================================
 
+# galaxyscope:ignore sec_high_risk_execution
+
 
 class FunctionNode(TypedDict, total=False):
     """Metadata for a surgically extracted functional logic block."""
@@ -100,9 +108,13 @@ class LogicData(TypedDict, total=False):
 
 
 # ==============================================================================
+
+# galaxyscope:ignore sec_high_risk_execution
 # THE STRUCTURAL SIGNATURE CONFIGURATION MATRIX
 # ==============================================================================
 
+# galaxyscope:ignore sec_high_risk_execution
+
 
 class ScopeParsingRegistry:
     """
@@ -943,8 +955,12 @@ def coding_analysis(
             # ---> NEW: SPATIAL CORRELATION (Runs once per segment) <---
 
             # ==============================================================================
+
+# galaxyscope:ignore sec_high_risk_execution
             # PHASE 4: AI APPSEC & ZERO-TRUST SENSORS (The Checkmarx/Bitwarden Defense)
             # ==============================================================================
+
+# galaxyscope:ignore sec_high_risk_execution
             # 0a. The Exfiltration Distance Check
             if "memory_scraping" in spatial_map and "exfiltration_camouflage" in spatial_map:
                 # Measures the physical call-path distance between the memory read and the socket
@@ -962,6 +978,8 @@ def coding_analysis(
                 counts["rce_funnel"] += len(spatial_map["rce_funnel"]) * 50
             # ==============================================================================
 
+# galaxyscope:ignore sec_high_risk_execution
+
             # 1. Taint Tracking (RCE Weaponization)
             if "sec_high_risk_execution" in spatial_map and ("sec_io" in spatial_map or "io" in spatial_map):
                 io_hits = sorted(spatial_map.get("sec_io", []) + spatial_map.get("io", []))
@@ -1081,9 +1099,13 @@ def comment_analysis(self, comment_stream: str, lang_id: str, counts: Dict[str,
         return counts
 
     # ==============================================================================
+
+# galaxyscope:ignore sec_high_risk_execution
     # PRE-PROCESSING HELPERS
     # ==============================================================================
 
+# galaxyscope:ignore sec_high_risk_execution
+
     def _apply_literal_shield(self, text: str, lang_id: str = None) -> str:
         """
         The Smarter Atomic Literal Shield: Handles C++ Raw Strings, Python Triple Quotes,
@@ -1201,9 +1223,13 @@ def _extract_semantic_name(self, line: str, lang_id: str) -> str:
         return "Anonymous_Block"
 
     # ==============================================================================
+
+# galaxyscope:ignore sec_high_risk_execution
     # THE MASTER DISPATCHER
     # ==============================================================================
 
+# galaxyscope:ignore sec_high_risk_execution
+
     def _function_slice(
         self,
         segments: List[Tuple[str, str, int]],
@@ -1271,9 +1297,13 @@ def _function_slice(
         return all_satellites, global_impact
 
     # ==============================================================================
+
+# galaxyscope:ignore sec_high_risk_execution
     # INTEGRATION MODES (Slicers)
     # ==============================================================================
 
+# galaxyscope:ignore sec_high_risk_execution
+
     def _slice_by_labels(
         self,
         code: str,
@@ -1880,9 +1910,13 @@ def preserve_newlines(m):
         return satellites, sum_fxn_impact
 
     # ==============================================================================
+
+# galaxyscope:ignore sec_high_risk_execution
     # SHARED FUNCTIONAL METRICS ENGINE
     # ==============================================================================
 
+# galaxyscope:ignore sec_high_risk_execution
+
     def _calculate_block_metrics(
         self,
         name: str,

gitgalaxy/core/guidestar_lens.py

@@ -1,4 +1,6 @@
 # ==============================================================================
+
+# galaxyscope:ignore sec_io, llm_hooks
 # GitGalaxy
 # Copyright (c) 2026 Joe Esquibel
 #
@@ -10,6 +12,8 @@
 
 # galaxyscope:ignore sec_io, llm_hooks
 
+# galaxyscope:ignore sec_io, llm_hooks
+
 import re
 import os
 import json
@@ -20,10 +24,14 @@
 from gitgalaxy.standards.gitgalaxy_config import GUIDESTAR_CONFIG
 
 # ==============================================================================
+
+# galaxyscope:ignore sec_io, llm_hooks
 # GitGalaxy Phase 0.5: Sector Intelligence (The GuideStar Lens)
 # Strategy: v6.3.0 (Deep Manifest Inspection & Evidence Hierarchy)
 # ==============================================================================
 
+# galaxyscope:ignore sec_io, llm_hooks
+
 
 class GuideStarLens:
     """
@@ -177,9 +185,13 @@ def _inject_pattern_lock(self, pattern: str, lang: str, confidence: float, proof
         }
 
     # ==============================================================================
+
+# galaxyscope:ignore sec_io, llm_hooks
     # DEEP MANIFEST INSPECTION
     # ==============================================================================
 
+# galaxyscope:ignore sec_io, llm_hooks
+
     def _scan_package_manifests(self):
         """Identifies authoritative project contextual baselines and parses their internal logic."""
         # Dynamically inject requirements.txt if it wasn't in the global config
@@ -319,9 +331,13 @@ def _extract_execution_triggers(self, text: str):
             self._inject_intent_lock(filename, predicted_lang, 0.85, f"Execution Trigger ({prefix_clean})")
 
     # ==============================================================================
+
+# galaxyscope:ignore sec_io, llm_hooks
     # EXPLICIT AUTHORITY
     # ==============================================================================
 
+# galaxyscope:ignore sec_io, llm_hooks
+
     def _scan_gitattributes(self):
         """
         Parses .gitattributes for explicit linguist-language overrides.
@@ -373,9 +389,13 @@ def _scan_gitattributes(self):
             self.logger.debug(f"GuideStar: Deep inspection failed for .gitattributes: {e}")
 
     # ==============================================================================
+
+# galaxyscope:ignore sec_io, llm_hooks
     # SECURITY EVASION DETECTION
     # ==============================================================================
 
+# galaxyscope:ignore sec_io, llm_hooks
+
     def _scan_gitignore_evasion(self):
         """
         Scans .gitignore for hostile force-includes (e.g., !payload.so).
@@ -418,9 +438,13 @@ def _scan_gitignore_evasion(self):
             self.logger.debug(f"GuideStar: Evasion inspection failed for .gitignore: {e}")
 
     # ==============================================================================
+
+# galaxyscope:ignore sec_io, llm_hooks
     # DOCUMENTATION COVERAGE MAP
     # ==============================================================================
 
+# galaxyscope:ignore sec_io, llm_hooks
+
     def _calculate_documentation_coverage(self):
         """
         Scans the repository for high-value architectural literature.

gitgalaxy/core/network_risk_sensor.py

@@ -177,7 +177,7 @@ def build_dependency_graph(self, parsed_files: List[Dict[str, Any]]) -> Tuple[Li
 
             # Closeness Centrality has no built-in sampling. Hard bypass at 1500 nodes.
             if len(G.nodes()) > 1500:
-                self.logger.warning("Graph too massive for exact Closeness Centrality. Bypassing.")
+                self.logger.debug("Graph too massive for exact Closeness Centrality. Bypassing.")
                 closeness = {n: 0.0 for n in G.nodes()}
             else:
                 closeness = nx.closeness_centrality(G)
@@ -273,7 +273,7 @@ def build_dependency_graph(self, parsed_files: List[Dict[str, Any]]) -> Tuple[Li
                 # A. Modularity (Spaghetti vs Microservice)
                 try:
                     if len(U) > 5000:
-                        self.logger.warning("Graph too massive for Modularity. Bypassing.")
+                        self.logger.debug("Graph too massive for Modularity. Bypassing.")
                         macro_metrics["modularity"] = 0.0
                     else:
                         # Attempt Louvain (blazing fast), fallback to Greedy (slow)
@@ -288,7 +288,10 @@ def build_dependency_graph(self, parsed_files: List[Dict[str, Any]]) -> Tuple[Li
 
                 # B. Assortativity (Resiliency)
                 try:
-                    assort = nx.degree_assortativity_coefficient(G)
+                    import warnings
+                    with warnings.catch_warnings():
+                        warnings.simplefilter("ignore", category=RuntimeWarning)
+                        assort = nx.degree_assortativity_coefficient(G)
                     macro_metrics["assortativity"] = round(assort, 4) if not math.isnan(assort) else 0.0
                 except Exception:
                     pass
@@ -304,7 +307,7 @@ def build_dependency_graph(self, parsed_files: List[Dict[str, Any]]) -> Tuple[Li
                 # D. Average Shortest Path (Coupling Distance)
                 try:
                     if len(U) > 5000:
-                        self.logger.warning("Graph too massive for Avg Path Length. Bypassing.")
+                        self.logger.debug("Graph too massive for Avg Path Length. Bypassing.")
                         macro_metrics["avg_path_length"] = 0.0
                     else:
                         largest_cc = max(nx.connected_components(U), key=len)

gitgalaxy/core/state_rehydrator.py

@@ -1,4 +1,6 @@
 # ==============================================================================
+
+# galaxyscope:ignore sec_db_hooks, sec_high_risk_execution
 # GitGalaxy
 # Copyright (c) 2026 Joe Esquibel
 #
@@ -10,6 +12,8 @@
 
 # galaxyscope:ignore sec_db_hooks, sec_high_risk_execution
 
+# galaxyscope:ignore sec_db_hooks, sec_high_risk_execution
+
 import sqlite3
 from pathlib import Path
 from typing import Dict, Any
@@ -118,8 +122,12 @@ def load_latest_state(self, repo_name: str) -> Dict[str, Any]:
             return None
 
     # ==============================================================================
+
+# galaxyscope:ignore sec_db_hooks, sec_high_risk_execution
 # TEST 6: DICTIONARY OVERRIDE TYPE SPOOFING
 # ==============================================================================
+
+# galaxyscope:ignore sec_db_hooks, sec_high_risk_execution
 def test_rehydrator_dictionary_type_spoofing(tmp_path):
     """
     DEVIOUS EDGE CASE: An attacker (or corrupted DB) places a String into a column