fix: relocate binary analysis skill

binary-analysis/scripts/binary_analysis/projects/diagnostics.py

@@ -0,0 +1,144 @@
+"""Diagnostics persistence — accumulate and retrieve diagnostics across commands.
+
+Diagnostics are persisted as JSONL in project/diagnostics.jsonl, one
+JSON object per line. Each entry has: severity, category, message, recoverable,
+command, and timestamp.
+
+The diagnostics file grows across the project lifecycle: warnings and errors
+from analyze, triage, suspicious-apis, and other commands are accumulated
+and retrievable via the `binary diagnostics` command.
+"""
+
+from __future__ import annotations
+
+import json
+import os
+from datetime import datetime, timezone
+from typing import Any
+
+from binary_analysis.projects.atomic import atomic_append_text
+
+DIAGNOSTICS_FILENAME = "diagnostics.jsonl"
+
+
+def _diagnostics_path(project_path: str) -> str:
+    """Return the path to the diagnostics file within a project workspace."""
+    return os.path.join(project_path, DIAGNOSTICS_FILENAME)
+
+
+def persist_diagnostics(
+    project_path: str,
+    diagnostics: list[dict[str, Any]],
+    command: str = "unknown",
+) -> None:
+    """Persist diagnostic entries to the project's diagnostics file.
+
+    Each diagnostic entry is augmented with a command field and timestamp
+    before being appended atomically to the JSONL file.
+
+    Args:
+        project_path: Absolute path to the project workspace directory.
+        diagnostics: List of diagnostic dicts to persist.
+        command: Name of the command that produced these diagnostics.
+    """
+    if not diagnostics:
+        return
+
+    path = _diagnostics_path(project_path)
+    timestamp = datetime.now(timezone.utc).isoformat()
+
+    for diag in diagnostics:
+        entry = {
+            "severity": diag.get("severity", "INFO"),
+            "category": diag.get("category", "general"),
+            "message": diag.get("message", ""),
+            "recoverable": diag.get("recoverable", True),
+            "command": command,
+            "timestamp": timestamp,
+        }
+        # Preserve optional fields
+        if "component" in diag:
+            entry["component"] = diag["component"]
+        if "remediation" in diag:
+            entry["remediation"] = diag["remediation"]
+
+        line = json.dumps(entry, ensure_ascii=False)
+        atomic_append_text(path, line)
+
+
+def load_diagnostics(project_path: str) -> list[dict[str, Any]]:
+    """Load all accumulated diagnostics from the project's diagnostics file.
+
+    Returns an empty list if the file does not exist or is empty.
+
+    Args:
+        project_path: Absolute path to the project workspace directory.
+
+    Returns:
+        List of diagnostic dicts ordered by appearance in the file
+        (oldest first).
+    """
+    path = _diagnostics_path(project_path)
+    if not os.path.exists(path):
+        return []
+
+    diagnostics: list[dict[str, Any]] = []
+    try:
+        with open(path, encoding="utf-8") as f:
+            for line_num, line in enumerate(f, start=1):
+                line = line.strip()
+                if not line:
+                    continue
+                try:
+                    entry = json.loads(line)
+                    diagnostics.append(entry)
+                except json.JSONDecodeError:
+                    # Skip corrupted lines but note in a diagnostic
+                    diagnostics.append(
+                        {
+                            "severity": "WARNING",
+                            "category": "diagnostics-file",
+                            "message": f"Corrupted diagnostics entry at line {line_num}",
+                            "recoverable": True,
+                            "command": "diagnostics",
+                            "timestamp": datetime.now(timezone.utc).isoformat(),
+                        }
+                    )
+    except OSError:
+        return []
+
+    return diagnostics
+
+
+def clear_diagnostics(project_path: str) -> None:
+    """Remove the diagnostics file (e.g., on project clean).
+
+    Args:
+        project_path: Absolute path to the project workspace directory.
+    """
+    path = _diagnostics_path(project_path)
+    if os.path.exists(path):
+        os.unlink(path)
+
+
+def get_diagnostics_summary(
+    diagnostics: list[dict[str, Any]],
+) -> dict[str, Any]:
+    """Compute a summary of diagnostic entries.
+
+    Args:
+        diagnostics: List of diagnostic dicts.
+
+    Returns:
+        Dict with total count and breakdown by severity.
+    """
+    by_severity: dict[str, int] = {"INFO": 0, "WARNING": 0, "ERROR": 0}
+    for d in diagnostics:
+        sev = d.get("severity", "INFO")
+        if sev in by_severity:
+            by_severity[sev] += 1
+
+    return {
+        "total": len(diagnostics),
+        "by_severity": by_severity,
+    }