diff --git a/tools/extract_pikeos_docs.py b/tools/extract_pikeos_docs.py
index 18550701b..16cf0e606 100644
--- a/tools/extract_pikeos_docs.py
+++ b/tools/extract_pikeos_docs.py
@@ -2,14 +2,14 @@
 """Extract PikeOS PDF manuals to markdown files.
 
 Usage:
-    python3 tools/extract_pikeos_docs.py <pdf> [<pdf> ...]
+    python3 tools/extract_pikeos_docs.py [--base-dir <dir>] <pdf> [<pdf> ...]
 
-Each PDF is converted to a markdown file under docs-extracted/ with the same
-relative path and YAML frontmatter containing title, source, and page count.
+Each PDF is converted to a markdown file under docs-extracted/ preserving the
+relative path from <dir> (default: docs/). YAML frontmatter contains title,
+source, category, and page count.
 """
 
 import argparse
-import os
 import re
 import subprocess
 import sys
@@ -18,7 +18,6 @@ from pathlib import Path
 
 
 REPO_ROOT = Path(__file__).resolve().parent.parent
-DOCS_DIR = REPO_ROOT / "docs"
 OUTPUT_DIR = REPO_ROOT / "docs-extracted"
 
 
@@ -46,9 +45,9 @@ def count_pages(pdf_path: Path) -> int:
     return 0
 
 
-def extract_pdf(pdf_path: Path) -> Path:
+def extract_pdf(pdf_path: Path, base_dir: Path) -> Path:
     """Extract a single PDF to a markdown file."""
-    rel_path = pdf_path.resolve().relative_to(DOCS_DIR.resolve())
+    rel_path = pdf_path.resolve().relative_to(base_dir.resolve())
     out_path = OUTPUT_DIR / rel_path.with_suffix(".md")
     out_path.parent.mkdir(parents=True, exist_ok=True)
 
@@ -56,6 +55,9 @@ def extract_pdf(pdf_path: Path) -> Path:
     pages = count_pages(pdf_path)
     category = rel_path.parent.as_posix() if rel_path.parent != Path(".") else "general"
 
+    source_prefix = base_dir.resolve().relative_to(REPO_ROOT).as_posix()
+    source_display = f"{source_prefix}/{rel_path.as_posix()}"
+
     # Extract plain text with layout preservation.
     text = subprocess.run(
         ["pdftotext", "-layout", "-nopgbrk", str(pdf_path), "-"],
@@ -69,7 +71,7 @@ def extract_pdf(pdf_path: Path) -> Path:
 
     frontmatter = f"""---
 title: "{title}"
-source: "docs/{rel_path.as_posix()}"
+source: "{source_display}"
 category: "{category}"
 pages: {pages}
 extracted: "{datetime.now().isoformat()}"
@@ -77,7 +79,7 @@ extracted: "{datetime.now().isoformat()}"
 
 # {title}
 
-> Extracted from `docs/{rel_path.as_posix()}` ({pages} pages).
+> Extracted from `{source_display}` ({pages} pages).
 > Figures, diagrams, and tables may not render accurately in plain text.
 
 {text}
@@ -89,6 +91,12 @@ extracted: "{datetime.now().isoformat()}"
 
 def main() -> int:
     parser = argparse.ArgumentParser(description="Extract PikeOS PDFs to markdown.")
+    parser.add_argument(
+        "--base-dir",
+        type=Path,
+        default=REPO_ROOT / "docs",
+        help="Base directory for resolving PDF relative paths (default: docs/)",
+    )
     parser.add_argument("pdfs", nargs="+", type=Path, help="PDF files to extract.")
     args = parser.parse_args()
 
@@ -99,7 +107,7 @@ def main() -> int:
             errors.append(f"Not found: {pdf}")
             continue
         try:
-            out = extract_pdf(pdf)
+            out = extract_pdf(pdf, args.base_dir)
             created.append(out)
             print(f"EXTRACTED: {out.relative_to(REPO_ROOT)}")
         except Exception as exc: