fix: check alternate paths before creating LEDGER.md/ARCHITECTURE.md stubs

Auditor and upgrader now check docs/LEDGER.md and docs/architecture/**
before reporting missing or creating stubs. Prevents duplicate files
when projects store these at non-standard paths.

Co-Authored-By: Oz <oz-agent@warp.dev>

Author: tbitcs

src/specsmith/auditor.py

@@ -79,11 +79,15 @@ def check_governance_files(root: Path) -> list[AuditResult]:
 
     for f in REQUIRED_FILES:
         path = root / f
+        found = path.exists()
+        # LEDGER.md: also check docs/LEDGER.md (some imported projects place it there)
+        if not found and f == "LEDGER.md":
+            found = (root / "docs" / "LEDGER.md").exists()
         results.append(
             AuditResult(
                 name=f"file-exists:{f}",
-                passed=path.exists(),
-                message=f"Required file {f} {'exists' if path.exists() else 'MISSING'}",
+                passed=found,
+                message=f"Required file {f} {'exists' if found else 'MISSING'}",
             )
         )
 
@@ -232,16 +236,20 @@ def check_ledger_health(root: Path) -> list[AuditResult]:
     """Check ledger quality and staleness."""
     results: list[AuditResult] = []
     ledger_path = root / "LEDGER.md"
-
     if not ledger_path.exists():
-        results.append(
-            AuditResult(
-                name="ledger-exists",
-                passed=False,
-                message="LEDGER.md not found",
+        # Also check docs/LEDGER.md (some imported projects place it there)
+        alt = root / "docs" / "LEDGER.md"
+        if alt.exists():
+            ledger_path = alt
+        else:
+            results.append(
+                AuditResult(
+                    name="ledger-exists",
+                    passed=False,
+                    message="LEDGER.md not found",
+                )
             )
-        )
-        return results
+            return results
 
     text = ledger_path.read_text(encoding="utf-8")
     lines = text.splitlines()

src/specsmith/upgrader.py

@@ -246,12 +246,20 @@ def _sync_full(
             out.write_text(tmpl.render(**ctx), encoding="utf-8")
             synced.append(f"{output_rel} (created)")
 
-    # 6. Essential docs — create stubs if missing (these are needed for audit to pass)
-    if not (root / "LEDGER.md").exists():
+    # 6. Essential docs — create stubs only if truly missing (check alternate paths)
+    has_ledger = (root / "LEDGER.md").exists() or (root / "docs" / "LEDGER.md").exists()
+    if not has_ledger:
         (root / "LEDGER.md").write_text("# Ledger\n\nNo entries yet.\n", encoding="utf-8")
         synced.append("LEDGER.md (created)")
 
-    if not (root / "docs" / "ARCHITECTURE.md").exists():
+    has_arch = (root / "docs" / "ARCHITECTURE.md").exists()
+    if not has_arch and (root / "docs").is_dir():
+        # Check subdirectories (e.g. docs/architecture/CPSC-RE-ARCHITECTURE.md)
+        has_arch = bool(
+            list((root / "docs").glob("**/architecture*"))
+            + list((root / "docs").glob("**/ARCHITECTURE*"))
+        )
+    if not has_arch:
         try:
             from specsmith.architect import generate_architecture
 
@@ -265,8 +273,6 @@ def _sync_full(
                 encoding="utf-8",
             )
             synced.append("docs/ARCHITECTURE.md (stub created)")
-
-    # Initialize credit tracking if not present
     specsmith_dir = root / ".specsmith"
     credit_budget = specsmith_dir / "credit-budget.json"
     if not credit_budget.exists():