skill: tell the user graphify-out/ is in their working tree (#3941)

Step 9's report never mentioned that graphify-out/ was written into the
working tree, so a repository that does not ignore it was left with
untracked machine-local files in git status and no explanation. The report
now adds one sentence in a git repository, with the two ways to handle it.

The note goes in the three core fragments (core, aider, devin); the devin
monolith change is sanctioned by a new round-trip predicate.

(cherry picked from commit b4e6769371)

graphify/skill-agents.md

@@ -648,6 +648,8 @@ If graphify saved you time, consider supporting it: https://github.com/sponsors/
 
 Replace PATH_TO_DIR with the actual absolute path of the directory that was processed.
 
+If PATH_TO_DIR is inside a git repository, add one line to the report: `graphify-out/` was written into the working tree, so unless the repository already ignores it, it will show in `git status`; the user can add `graphify-out/` to `.gitignore`, or commit only the outputs their team should share (see https://docs.graphify.com/guides/team-workflows).
+
 Then paste these sections from GRAPH_REPORT.md directly into the chat:
 - God Nodes
 - Surprising Connections

graphify/skill-aider.md

@@ -747,6 +747,8 @@ If graphify saved you time, consider supporting it: https://github.com/sponsors/
 
 Replace PATH_TO_DIR with the actual absolute path of the directory that was processed.
 
+If PATH_TO_DIR is inside a git repository, add one line to the report: `graphify-out/` was written into the working tree, so unless the repository already ignores it, it will show in `git status`; the user can add `graphify-out/` to `.gitignore`, or commit only the outputs their team should share (see https://docs.graphify.com/guides/team-workflows).
+
 Then paste these sections from GRAPH_REPORT.md directly into the chat:
 - God Nodes
 - Surprising Connections

graphify/skill-amp.md

@@ -648,6 +648,8 @@ If graphify saved you time, consider supporting it: https://github.com/sponsors/
 
 Replace PATH_TO_DIR with the actual absolute path of the directory that was processed.
 
+If PATH_TO_DIR is inside a git repository, add one line to the report: `graphify-out/` was written into the working tree, so unless the repository already ignores it, it will show in `git status`; the user can add `graphify-out/` to `.gitignore`, or commit only the outputs their team should share (see https://docs.graphify.com/guides/team-workflows).
+
 Then paste these sections from GRAPH_REPORT.md directly into the chat:
 - God Nodes
 - Surprising Connections

graphify/skill-claw.md

@@ -651,6 +651,8 @@ If graphify saved you time, consider supporting it: https://github.com/sponsors/
 
 Replace PATH_TO_DIR with the actual absolute path of the directory that was processed.
 
+If PATH_TO_DIR is inside a git repository, add one line to the report: `graphify-out/` was written into the working tree, so unless the repository already ignores it, it will show in `git status`; the user can add `graphify-out/` to `.gitignore`, or commit only the outputs their team should share (see https://docs.graphify.com/guides/team-workflows).
+
 Then paste these sections from GRAPH_REPORT.md directly into the chat:
 - God Nodes
 - Surprising Connections

graphify/skill-codex.md

@@ -648,6 +648,8 @@ If graphify saved you time, consider supporting it: https://github.com/sponsors/
 
 Replace PATH_TO_DIR with the actual absolute path of the directory that was processed.
 
+If PATH_TO_DIR is inside a git repository, add one line to the report: `graphify-out/` was written into the working tree, so unless the repository already ignores it, it will show in `git status`; the user can add `graphify-out/` to `.gitignore`, or commit only the outputs their team should share (see https://docs.graphify.com/guides/team-workflows).
+
 Then paste these sections from GRAPH_REPORT.md directly into the chat:
 - God Nodes
 - Surprising Connections

graphify/skill-copilot.md

@@ -651,6 +651,8 @@ If graphify saved you time, consider supporting it: https://github.com/sponsors/
 
 Replace PATH_TO_DIR with the actual absolute path of the directory that was processed.
 
+If PATH_TO_DIR is inside a git repository, add one line to the report: `graphify-out/` was written into the working tree, so unless the repository already ignores it, it will show in `git status`; the user can add `graphify-out/` to `.gitignore`, or commit only the outputs their team should share (see https://docs.graphify.com/guides/team-workflows).
+
 Then paste these sections from GRAPH_REPORT.md directly into the chat:
 - God Nodes
 - Surprising Connections

graphify/skill-devin.md

@@ -866,6 +866,8 @@ If graphify saved you time, consider supporting it: https://github.com/sponsors/
 
 Replace PATH_TO_DIR with the actual absolute path of the directory that was processed.
 
+If PATH_TO_DIR is inside a git repository, add one line to the report: `graphify-out/` was written into the working tree, so unless the repository already ignores it, it will show in `git status`; the user can add `graphify-out/` to `.gitignore`, or commit only the outputs their team should share (see https://docs.graphify.com/guides/team-workflows).
+
 Then paste these sections from GRAPH_REPORT.md directly into the chat:
 - God Nodes
 - Surprising Connections

graphify/skill-droid.md

@@ -648,6 +648,8 @@ If graphify saved you time, consider supporting it: https://github.com/sponsors/
 
 Replace PATH_TO_DIR with the actual absolute path of the directory that was processed.
 
+If PATH_TO_DIR is inside a git repository, add one line to the report: `graphify-out/` was written into the working tree, so unless the repository already ignores it, it will show in `git status`; the user can add `graphify-out/` to `.gitignore`, or commit only the outputs their team should share (see https://docs.graphify.com/guides/team-workflows).
+
 Then paste these sections from GRAPH_REPORT.md directly into the chat:
 - God Nodes
 - Surprising Connections

graphify/skill-kilo.md

@@ -651,6 +651,8 @@ If graphify saved you time, consider supporting it: https://github.com/sponsors/
 
 Replace PATH_TO_DIR with the actual absolute path of the directory that was processed.
 
+If PATH_TO_DIR is inside a git repository, add one line to the report: `graphify-out/` was written into the working tree, so unless the repository already ignores it, it will show in `git status`; the user can add `graphify-out/` to `.gitignore`, or commit only the outputs their team should share (see https://docs.graphify.com/guides/team-workflows).
+
 Then paste these sections from GRAPH_REPORT.md directly into the chat:
 - God Nodes
 - Surprising Connections

graphify/skill-kiro.md

@@ -651,6 +651,8 @@ If graphify saved you time, consider supporting it: https://github.com/sponsors/
 
 Replace PATH_TO_DIR with the actual absolute path of the directory that was processed.
 
+If PATH_TO_DIR is inside a git repository, add one line to the report: `graphify-out/` was written into the working tree, so unless the repository already ignores it, it will show in `git status`; the user can add `graphify-out/` to `.gitignore`, or commit only the outputs their team should share (see https://docs.graphify.com/guides/team-workflows).
+
 Then paste these sections from GRAPH_REPORT.md directly into the chat:
 - God Nodes
 - Surprising Connections

graphify/skill-opencode.md

@@ -643,6 +643,8 @@ If graphify saved you time, consider supporting it: https://github.com/sponsors/
 
 Replace PATH_TO_DIR with the actual absolute path of the directory that was processed.
 
+If PATH_TO_DIR is inside a git repository, add one line to the report: `graphify-out/` was written into the working tree, so unless the repository already ignores it, it will show in `git status`; the user can add `graphify-out/` to `.gitignore`, or commit only the outputs their team should share (see https://docs.graphify.com/guides/team-workflows).
+
 Then paste these sections from GRAPH_REPORT.md directly into the chat:
 - God Nodes
 - Surprising Connections

graphify/skill-pi.md

@@ -651,6 +651,8 @@ If graphify saved you time, consider supporting it: https://github.com/sponsors/
 
 Replace PATH_TO_DIR with the actual absolute path of the directory that was processed.
 
+If PATH_TO_DIR is inside a git repository, add one line to the report: `graphify-out/` was written into the working tree, so unless the repository already ignores it, it will show in `git status`; the user can add `graphify-out/` to `.gitignore`, or commit only the outputs their team should share (see https://docs.graphify.com/guides/team-workflows).
+
 Then paste these sections from GRAPH_REPORT.md directly into the chat:
 - God Nodes
 - Surprising Connections

graphify/skill-trae.md

@@ -649,6 +649,8 @@ If graphify saved you time, consider supporting it: https://github.com/sponsors/
 
 Replace PATH_TO_DIR with the actual absolute path of the directory that was processed.
 
+If PATH_TO_DIR is inside a git repository, add one line to the report: `graphify-out/` was written into the working tree, so unless the repository already ignores it, it will show in `git status`; the user can add `graphify-out/` to `.gitignore`, or commit only the outputs their team should share (see https://docs.graphify.com/guides/team-workflows).
+
 Then paste these sections from GRAPH_REPORT.md directly into the chat:
 - God Nodes
 - Surprising Connections

graphify/skill-vscode.md

@@ -647,6 +647,8 @@ If graphify saved you time, consider supporting it: https://github.com/sponsors/
 
 Replace PATH_TO_DIR with the actual absolute path of the directory that was processed.
 
+If PATH_TO_DIR is inside a git repository, add one line to the report: `graphify-out/` was written into the working tree, so unless the repository already ignores it, it will show in `git status`; the user can add `graphify-out/` to `.gitignore`, or commit only the outputs their team should share (see https://docs.graphify.com/guides/team-workflows).
+
 Then paste these sections from GRAPH_REPORT.md directly into the chat:
 - God Nodes
 - Surprising Connections

graphify/skill-windows.md

@@ -679,6 +679,8 @@ If graphify saved you time, consider supporting it: https://github.com/sponsors/
 
 Replace PATH_TO_DIR with the actual absolute path of the directory that was processed.
 
+If PATH_TO_DIR is inside a git repository, add one line to the report: `graphify-out/` was written into the working tree, so unless the repository already ignores it, it will show in `git status`; the user can add `graphify-out/` to `.gitignore`, or commit only the outputs their team should share (see https://docs.graphify.com/guides/team-workflows).
+
 Then paste these sections from GRAPH_REPORT.md directly into the chat:
 - God Nodes
 - Surprising Connections

graphify/skill.md

@@ -651,6 +651,8 @@ If graphify saved you time, consider supporting it: https://github.com/sponsors/
 
 Replace PATH_TO_DIR with the actual absolute path of the directory that was processed.
 
+If PATH_TO_DIR is inside a git repository, add one line to the report: `graphify-out/` was written into the working tree, so unless the repository already ignores it, it will show in `git status`; the user can add `graphify-out/` to `.gitignore`, or commit only the outputs their team should share (see https://docs.graphify.com/guides/team-workflows).
+
 Then paste these sections from GRAPH_REPORT.md directly into the chat:
 - God Nodes
 - Surprising Connections

tools/skillgen/expected/graphify__skill-agents.md

@@ -648,6 +648,8 @@ If graphify saved you time, consider supporting it: https://github.com/sponsors/
 
 Replace PATH_TO_DIR with the actual absolute path of the directory that was processed.
 
+If PATH_TO_DIR is inside a git repository, add one line to the report: `graphify-out/` was written into the working tree, so unless the repository already ignores it, it will show in `git status`; the user can add `graphify-out/` to `.gitignore`, or commit only the outputs their team should share (see https://docs.graphify.com/guides/team-workflows).
+
 Then paste these sections from GRAPH_REPORT.md directly into the chat:
 - God Nodes
 - Surprising Connections

tools/skillgen/expected/graphify__skill-aider.md

@@ -747,6 +747,8 @@ If graphify saved you time, consider supporting it: https://github.com/sponsors/
 
 Replace PATH_TO_DIR with the actual absolute path of the directory that was processed.
 
+If PATH_TO_DIR is inside a git repository, add one line to the report: `graphify-out/` was written into the working tree, so unless the repository already ignores it, it will show in `git status`; the user can add `graphify-out/` to `.gitignore`, or commit only the outputs their team should share (see https://docs.graphify.com/guides/team-workflows).
+
 Then paste these sections from GRAPH_REPORT.md directly into the chat:
 - God Nodes
 - Surprising Connections

tools/skillgen/expected/graphify__skill-amp.md

@@ -648,6 +648,8 @@ If graphify saved you time, consider supporting it: https://github.com/sponsors/
 
 Replace PATH_TO_DIR with the actual absolute path of the directory that was processed.
 
+If PATH_TO_DIR is inside a git repository, add one line to the report: `graphify-out/` was written into the working tree, so unless the repository already ignores it, it will show in `git status`; the user can add `graphify-out/` to `.gitignore`, or commit only the outputs their team should share (see https://docs.graphify.com/guides/team-workflows).
+
 Then paste these sections from GRAPH_REPORT.md directly into the chat:
 - God Nodes
 - Surprising Connections

tools/skillgen/expected/graphify__skill-claw.md

@@ -651,6 +651,8 @@ If graphify saved you time, consider supporting it: https://github.com/sponsors/
 
 Replace PATH_TO_DIR with the actual absolute path of the directory that was processed.
 
+If PATH_TO_DIR is inside a git repository, add one line to the report: `graphify-out/` was written into the working tree, so unless the repository already ignores it, it will show in `git status`; the user can add `graphify-out/` to `.gitignore`, or commit only the outputs their team should share (see https://docs.graphify.com/guides/team-workflows).
+
 Then paste these sections from GRAPH_REPORT.md directly into the chat:
 - God Nodes
 - Surprising Connections

tools/skillgen/expected/graphify__skill-codex.md

@@ -648,6 +648,8 @@ If graphify saved you time, consider supporting it: https://github.com/sponsors/
 
 Replace PATH_TO_DIR with the actual absolute path of the directory that was processed.
 
+If PATH_TO_DIR is inside a git repository, add one line to the report: `graphify-out/` was written into the working tree, so unless the repository already ignores it, it will show in `git status`; the user can add `graphify-out/` to `.gitignore`, or commit only the outputs their team should share (see https://docs.graphify.com/guides/team-workflows).
+
 Then paste these sections from GRAPH_REPORT.md directly into the chat:
 - God Nodes
 - Surprising Connections

tools/skillgen/expected/graphify__skill-copilot.md

@@ -651,6 +651,8 @@ If graphify saved you time, consider supporting it: https://github.com/sponsors/
 
 Replace PATH_TO_DIR with the actual absolute path of the directory that was processed.
 
+If PATH_TO_DIR is inside a git repository, add one line to the report: `graphify-out/` was written into the working tree, so unless the repository already ignores it, it will show in `git status`; the user can add `graphify-out/` to `.gitignore`, or commit only the outputs their team should share (see https://docs.graphify.com/guides/team-workflows).
+
 Then paste these sections from GRAPH_REPORT.md directly into the chat:
 - God Nodes
 - Surprising Connections

tools/skillgen/expected/graphify__skill-devin.md

@@ -866,6 +866,8 @@ If graphify saved you time, consider supporting it: https://github.com/sponsors/
 
 Replace PATH_TO_DIR with the actual absolute path of the directory that was processed.
 
+If PATH_TO_DIR is inside a git repository, add one line to the report: `graphify-out/` was written into the working tree, so unless the repository already ignores it, it will show in `git status`; the user can add `graphify-out/` to `.gitignore`, or commit only the outputs their team should share (see https://docs.graphify.com/guides/team-workflows).
+
 Then paste these sections from GRAPH_REPORT.md directly into the chat:
 - God Nodes
 - Surprising Connections

tools/skillgen/expected/graphify__skill-droid.md

@@ -648,6 +648,8 @@ If graphify saved you time, consider supporting it: https://github.com/sponsors/
 
 Replace PATH_TO_DIR with the actual absolute path of the directory that was processed.
 
+If PATH_TO_DIR is inside a git repository, add one line to the report: `graphify-out/` was written into the working tree, so unless the repository already ignores it, it will show in `git status`; the user can add `graphify-out/` to `.gitignore`, or commit only the outputs their team should share (see https://docs.graphify.com/guides/team-workflows).
+
 Then paste these sections from GRAPH_REPORT.md directly into the chat:
 - God Nodes
 - Surprising Connections

tools/skillgen/expected/graphify__skill-kilo.md

@@ -651,6 +651,8 @@ If graphify saved you time, consider supporting it: https://github.com/sponsors/
 
 Replace PATH_TO_DIR with the actual absolute path of the directory that was processed.
 
+If PATH_TO_DIR is inside a git repository, add one line to the report: `graphify-out/` was written into the working tree, so unless the repository already ignores it, it will show in `git status`; the user can add `graphify-out/` to `.gitignore`, or commit only the outputs their team should share (see https://docs.graphify.com/guides/team-workflows).
+
 Then paste these sections from GRAPH_REPORT.md directly into the chat:
 - God Nodes
 - Surprising Connections

tools/skillgen/expected/graphify__skill-kiro.md

@@ -651,6 +651,8 @@ If graphify saved you time, consider supporting it: https://github.com/sponsors/
 
 Replace PATH_TO_DIR with the actual absolute path of the directory that was processed.
 
+If PATH_TO_DIR is inside a git repository, add one line to the report: `graphify-out/` was written into the working tree, so unless the repository already ignores it, it will show in `git status`; the user can add `graphify-out/` to `.gitignore`, or commit only the outputs their team should share (see https://docs.graphify.com/guides/team-workflows).
+
 Then paste these sections from GRAPH_REPORT.md directly into the chat:
 - God Nodes
 - Surprising Connections

tools/skillgen/expected/graphify__skill-opencode.md

@@ -643,6 +643,8 @@ If graphify saved you time, consider supporting it: https://github.com/sponsors/
 
 Replace PATH_TO_DIR with the actual absolute path of the directory that was processed.
 
+If PATH_TO_DIR is inside a git repository, add one line to the report: `graphify-out/` was written into the working tree, so unless the repository already ignores it, it will show in `git status`; the user can add `graphify-out/` to `.gitignore`, or commit only the outputs their team should share (see https://docs.graphify.com/guides/team-workflows).
+
 Then paste these sections from GRAPH_REPORT.md directly into the chat:
 - God Nodes
 - Surprising Connections

tools/skillgen/expected/graphify__skill-pi.md

@@ -651,6 +651,8 @@ If graphify saved you time, consider supporting it: https://github.com/sponsors/
 
 Replace PATH_TO_DIR with the actual absolute path of the directory that was processed.
 
+If PATH_TO_DIR is inside a git repository, add one line to the report: `graphify-out/` was written into the working tree, so unless the repository already ignores it, it will show in `git status`; the user can add `graphify-out/` to `.gitignore`, or commit only the outputs their team should share (see https://docs.graphify.com/guides/team-workflows).
+
 Then paste these sections from GRAPH_REPORT.md directly into the chat:
 - God Nodes
 - Surprising Connections

tools/skillgen/expected/graphify__skill-trae.md

@@ -649,6 +649,8 @@ If graphify saved you time, consider supporting it: https://github.com/sponsors/
 
 Replace PATH_TO_DIR with the actual absolute path of the directory that was processed.
 
+If PATH_TO_DIR is inside a git repository, add one line to the report: `graphify-out/` was written into the working tree, so unless the repository already ignores it, it will show in `git status`; the user can add `graphify-out/` to `.gitignore`, or commit only the outputs their team should share (see https://docs.graphify.com/guides/team-workflows).
+
 Then paste these sections from GRAPH_REPORT.md directly into the chat:
 - God Nodes
 - Surprising Connections

tools/skillgen/expected/graphify__skill-vscode.md

@@ -647,6 +647,8 @@ If graphify saved you time, consider supporting it: https://github.com/sponsors/
 
 Replace PATH_TO_DIR with the actual absolute path of the directory that was processed.
 
+If PATH_TO_DIR is inside a git repository, add one line to the report: `graphify-out/` was written into the working tree, so unless the repository already ignores it, it will show in `git status`; the user can add `graphify-out/` to `.gitignore`, or commit only the outputs their team should share (see https://docs.graphify.com/guides/team-workflows).
+
 Then paste these sections from GRAPH_REPORT.md directly into the chat:
 - God Nodes
 - Surprising Connections

tools/skillgen/expected/graphify__skill-windows.md

@@ -679,6 +679,8 @@ If graphify saved you time, consider supporting it: https://github.com/sponsors/
 
 Replace PATH_TO_DIR with the actual absolute path of the directory that was processed.
 
+If PATH_TO_DIR is inside a git repository, add one line to the report: `graphify-out/` was written into the working tree, so unless the repository already ignores it, it will show in `git status`; the user can add `graphify-out/` to `.gitignore`, or commit only the outputs their team should share (see https://docs.graphify.com/guides/team-workflows).
+
 Then paste these sections from GRAPH_REPORT.md directly into the chat:
 - God Nodes
 - Surprising Connections

tools/skillgen/expected/graphify__skill.md

@@ -651,6 +651,8 @@ If graphify saved you time, consider supporting it: https://github.com/sponsors/
 
 Replace PATH_TO_DIR with the actual absolute path of the directory that was processed.
 
+If PATH_TO_DIR is inside a git repository, add one line to the report: `graphify-out/` was written into the working tree, so unless the repository already ignores it, it will show in `git status`; the user can add `graphify-out/` to `.gitignore`, or commit only the outputs their team should share (see https://docs.graphify.com/guides/team-workflows).
+
 Then paste these sections from GRAPH_REPORT.md directly into the chat:
 - God Nodes
 - Surprising Connections

tools/skillgen/fragments/core/aider.md

@@ -747,6 +747,8 @@ If graphify saved you time, consider supporting it: https://github.com/sponsors/
 
 Replace PATH_TO_DIR with the actual absolute path of the directory that was processed.
 
+If PATH_TO_DIR is inside a git repository, add one line to the report: `graphify-out/` was written into the working tree, so unless the repository already ignores it, it will show in `git status`; the user can add `graphify-out/` to `.gitignore`, or commit only the outputs their team should share (see https://docs.graphify.com/guides/team-workflows).
+
 Then paste these sections from GRAPH_REPORT.md directly into the chat:
 - God Nodes
 - Surprising Connections

tools/skillgen/fragments/core/core.md

@@ -580,6 +580,8 @@ If graphify saved you time, consider supporting it: https://github.com/sponsors/
 
 Replace PATH_TO_DIR with the actual absolute path of the directory that was processed.
 
+If PATH_TO_DIR is inside a git repository, add one line to the report: `graphify-out/` was written into the working tree, so unless the repository already ignores it, it will show in `git status`; the user can add `graphify-out/` to `.gitignore`, or commit only the outputs their team should share (see https://docs.graphify.com/guides/team-workflows).
+
 Then paste these sections from GRAPH_REPORT.md directly into the chat:
 - God Nodes
 - Surprising Connections

tools/skillgen/fragments/core/devin.md

@@ -866,6 +866,8 @@ If graphify saved you time, consider supporting it: https://github.com/sponsors/
 
 Replace PATH_TO_DIR with the actual absolute path of the directory that was processed.
 
+If PATH_TO_DIR is inside a git repository, add one line to the report: `graphify-out/` was written into the working tree, so unless the repository already ignores it, it will show in `git status`; the user can add `graphify-out/` to `.gitignore`, or commit only the outputs their team should share (see https://docs.graphify.com/guides/team-workflows).
+
 Then paste these sections from GRAPH_REPORT.md directly into the chat:
 - God Nodes
 - Surprising Connections

tools/skillgen/gen.py

@@ -1209,6 +1209,17 @@ def _is_persisted_scan_options_fix_line(line: str) -> bool:
     )
 
 
+def _is_worktree_visibility_note_line(line: str) -> bool:
+    """Whether a line is the Step 9 working-tree note (#3941).
+
+    Step 9's report never told the user that ``graphify-out/`` was written into
+    their working tree, so a repository that does not ignore it was left with
+    untracked machine-local files in ``git status`` and no explanation. The report
+    now adds one sentence saying so, with the two ways to handle it.
+    """
+    return "`graphify-out/` was written into the working tree" in line
+
+
 # Every line that may differ between a rendered monolith and its pristine v8
 # baseline. Each predicate documents one sanctioned change-class; a blank line is
 # allowed because the multi-line fix blocks insert spacing. Anything else failing
@@ -1234,6 +1245,7 @@ _SANCTIONED_MONOLITH_DIFFS = (
     _is_watch_injection_fix_line,
     _is_graph_diff_direction_fix_line,
     _is_persisted_scan_options_fix_line,
+    _is_worktree_visibility_note_line,
 )