skill: fast path for existing graphs, fix large-corpus gate, fix subfolder output

- Fast path: if graphify-out/graph.json exists and user is asking a question
  (not an explicit rebuild), skip detect entirely and run graphify query —
  prevents the skill from refusing large already-built corpora (#930)
- Raise FILE_COUNT_UPPER 200 → 500 so typical 200-500 file codebases no longer
  hit the large-corpus size gate on fresh extraction (#930)
- Subdirectory breakdown now strips the scan-root prefix so agent shows
  relative names (core/, service/) not absolute paths rooted at / (#930)
- Document multi-subfolder CLI pattern: graphify extract ./sub/ places
  graphify-out/ inside each subfolder; skill clobbers single root graphify-out
  when run on subfolders separately (#930)

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

graphify/detect.py

@@ -33,7 +33,7 @@ VIDEO_EXTENSIONS = {'.mp4', '.mov', '.webm', '.mkv', '.avi', '.m4v', '.mp3', '.w
 
 CORPUS_WARN_THRESHOLD = 50_000    # words - below this, warn "you may not need a graph"
 CORPUS_UPPER_THRESHOLD = 500_000  # words - above this, warn about token cost
-FILE_COUNT_UPPER = 200             # files - above this, warn about token cost
+FILE_COUNT_UPPER = 500             # files - above this, warn about token cost
 
 # Parent directories whose contents are always sensitive.
 # Checked against path.parts[:-1] (parents only) so a root-level file named

graphify/skill.md

@@ -49,6 +49,8 @@ Drop any folder of code, docs, papers, images, or video into graphify and get a
 
 If the user invoked `/graphify --help` or `/graphify -h` (with no other arguments), print the contents of the `## Usage` section above verbatim and stop. Do not run any commands, do not detect files, do not default the path to `.`. Just print the Usage block and return.
 
+**Fast path — existing graph:** Before doing anything else, check whether `graphify-out/graph.json` already exists in the current directory. If it does AND the user's request is a natural-language question about the codebase (e.g. "How does X work?", "What calls Y?", "Trace the data flow through Z") and NOT an explicit rebuild command (`--update`, `--cluster-only`, or a bare path/URL that implies fresh extraction): **skip Steps 1–5 entirely and jump straight to `## For /graphify query`.** Run `graphify query "<question>"` immediately. Do not run detect. Do not check corpus size. Do not ask the user to narrow. The graph is already built — use it.
+
 If no path was given, use `.` (current directory). Do not ask the user for a path.
 
 If the path argument starts with `https://github.com/` or `http://github.com/`, treat it as a GitHub URL - run Step 0 before anything else, then continue with the resolved local path.
@@ -78,6 +80,25 @@ graphify merge-graphs \
 
 Graphify clones into `~/.graphify/repos/<owner>/<repo>` and reuses existing clones on repeat runs. Each node in the merged graph carries a `repo` attribute so you can filter by origin.
 
+**Multiple local subfolders (monorepo or multi-service layout):**
+
+The skill pipeline writes all intermediate and final outputs to `graphify-out/` in the current working directory. Running the skill on each subfolder separately will clobber the same output dir. Instead, use the CLI directly for each subfolder — it places `graphify-out/` *inside* the scanned path:
+
+```bash
+graphify extract ./core/     --backend gemini  # → ./core/graphify-out/graph.json
+graphify extract ./service/  --backend gemini  # → ./service/graphify-out/graph.json
+graphify extract ./platform/ --backend gemini  # → ./platform/graphify-out/graph.json
+
+# Then merge at the project root:
+graphify merge-graphs \
+  ./core/graphify-out/graph.json \
+  ./service/graphify-out/graph.json \
+  ./platform/graphify-out/graph.json \
+  --out graphify-out/graph.json
+```
+
+Once `graphify-out/graph.json` exists, the fast path above takes over: any codebase question runs `graphify query` directly on the merged graph — no re-extraction, no size gate.
+
 ### Step 1 - Ensure graphify is installed
 
 ```bash
@@ -148,7 +169,7 @@ Omit any category with 0 files from the summary.
 Then act on it:
 - If `total_files` is 0: stop with "No supported files found in [path]."
 - If `skipped_sensitive` is non-empty: mention file count skipped, not the file names.
-- If `total_words` > 2,000,000 OR `total_files` > 200: show the warning and the top 5 subdirectories by file count, then ask which subfolder to run on. Wait for the user's answer before proceeding.
+- If `total_words` > 2,000,000 OR `total_files` > 500: show the warning. Then compute the top 5 subdirectories by file count using **relative paths from INPUT_PATH** (strip the absolute scan-root prefix so you show `core/`, `service/`, not `/home/user/project/core/`), show those, then ask which subfolder to run on. Wait for the user's answer before proceeding.
 - Otherwise: proceed directly to Step 2.5 if video files were detected, or Step 3 if not.
 
 ### Step 2.5 - Transcribe video / audio files (only if video files detected)