diff --git a/graphify/skill-agents.md b/graphify/skill-agents.md
index 190827d9a..d3d4a2869 100644
--- a/graphify/skill-agents.md
+++ b/graphify/skill-agents.md
@@ -617,7 +617,7 @@ print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_t
 "
 rm -f graphify-out/.graphify_detect.json graphify-out/.graphify_extract.json graphify-out/.graphify_ast.json graphify-out/.graphify_semantic.json graphify-out/.graphify_analysis.json
 find graphify-out -maxdepth 1 -name '.graphify_chunk_*.json' -delete 2>/dev/null
-rm -f graphify-out/.needs_update 2>/dev/null || true
+rm -f graphify-out/needs_update 2>/dev/null || true
 ```
 
 Replace INPUT_PATH with the actual path (same value used in Steps 4-5) so the manifest is relativized to the scan root.
diff --git a/graphify/skill-aider.md b/graphify/skill-aider.md
index 4996beb78..d0c308b8f 100644
--- a/graphify/skill-aider.md
+++ b/graphify/skill-aider.md
@@ -720,7 +720,7 @@ print(f'This run: {input_tok:,} input tokens, {output_tok:,} output tokens')
 print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_tokens\"]:,} output ({len(cost[\"runs\"])} runs)')
 "
 rm -f .graphify_detect.json .graphify_extract.json .graphify_ast.json .graphify_semantic.json .graphify_analysis.json .graphify_labels.json; find . -maxdepth 1 -name '.graphify_chunk_*.json' -delete 2>/dev/null
-rm -f graphify-out/.needs_update 2>/dev/null || true
+rm -f graphify-out/needs_update 2>/dev/null || true
 ```
 
 Tell the user (omit the obsidian line unless --obsidian was given):
diff --git a/graphify/skill-amp.md b/graphify/skill-amp.md
index 190827d9a..d3d4a2869 100644
--- a/graphify/skill-amp.md
+++ b/graphify/skill-amp.md
@@ -617,7 +617,7 @@ print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_t
 "
 rm -f graphify-out/.graphify_detect.json graphify-out/.graphify_extract.json graphify-out/.graphify_ast.json graphify-out/.graphify_semantic.json graphify-out/.graphify_analysis.json
 find graphify-out -maxdepth 1 -name '.graphify_chunk_*.json' -delete 2>/dev/null
-rm -f graphify-out/.needs_update 2>/dev/null || true
+rm -f graphify-out/needs_update 2>/dev/null || true
 ```
 
 Replace INPUT_PATH with the actual path (same value used in Steps 4-5) so the manifest is relativized to the scan root.
diff --git a/graphify/skill-claw.md b/graphify/skill-claw.md
index abd2811d2..a65de35b4 100644
--- a/graphify/skill-claw.md
+++ b/graphify/skill-claw.md
@@ -620,7 +620,7 @@ print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_t
 "
 rm -f graphify-out/.graphify_detect.json graphify-out/.graphify_extract.json graphify-out/.graphify_ast.json graphify-out/.graphify_semantic.json graphify-out/.graphify_analysis.json
 find graphify-out -maxdepth 1 -name '.graphify_chunk_*.json' -delete 2>/dev/null
-rm -f graphify-out/.needs_update 2>/dev/null || true
+rm -f graphify-out/needs_update 2>/dev/null || true
 ```
 
 Replace INPUT_PATH with the actual path (same value used in Steps 4-5) so the manifest is relativized to the scan root.
diff --git a/graphify/skill-codex.md b/graphify/skill-codex.md
index af3f723c7..42e0bd473 100644
--- a/graphify/skill-codex.md
+++ b/graphify/skill-codex.md
@@ -617,7 +617,7 @@ print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_t
 "
 rm -f graphify-out/.graphify_detect.json graphify-out/.graphify_extract.json graphify-out/.graphify_ast.json graphify-out/.graphify_semantic.json graphify-out/.graphify_analysis.json
 find graphify-out -maxdepth 1 -name '.graphify_chunk_*.json' -delete 2>/dev/null
-rm -f graphify-out/.needs_update 2>/dev/null || true
+rm -f graphify-out/needs_update 2>/dev/null || true
 ```
 
 Replace INPUT_PATH with the actual path (same value used in Steps 4-5) so the manifest is relativized to the scan root.
diff --git a/graphify/skill-copilot.md b/graphify/skill-copilot.md
index abd2811d2..a65de35b4 100644
--- a/graphify/skill-copilot.md
+++ b/graphify/skill-copilot.md
@@ -620,7 +620,7 @@ print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_t
 "
 rm -f graphify-out/.graphify_detect.json graphify-out/.graphify_extract.json graphify-out/.graphify_ast.json graphify-out/.graphify_semantic.json graphify-out/.graphify_analysis.json
 find graphify-out -maxdepth 1 -name '.graphify_chunk_*.json' -delete 2>/dev/null
-rm -f graphify-out/.needs_update 2>/dev/null || true
+rm -f graphify-out/needs_update 2>/dev/null || true
 ```
 
 Replace INPUT_PATH with the actual path (same value used in Steps 4-5) so the manifest is relativized to the scan root.
diff --git a/graphify/skill-devin.md b/graphify/skill-devin.md
index f9be846cb..5d720b633 100644
--- a/graphify/skill-devin.md
+++ b/graphify/skill-devin.md
@@ -838,7 +838,7 @@ print(f'This run: {input_tok:,} input tokens, {output_tok:,} output tokens')
 print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_tokens\"]:,} output ({len(cost[\"runs\"])} runs)')
 "
 rm -f graphify-out/.graphify_detect.json graphify-out/.graphify_extract.json graphify-out/.graphify_ast.json graphify-out/.graphify_semantic.json graphify-out/.graphify_analysis.json graphify-out/.graphify_labels.json graphify-out/.graphify_incremental.json graphify-out/.graphify_transcripts.json graphify-out/.graphify_old.json; find graphify-out -maxdepth 1 -name '.graphify_chunk_*.json' -delete 2>/dev/null
-rm -f graphify-out/.needs_update 2>/dev/null || true
+rm -f graphify-out/needs_update 2>/dev/null || true
 ```
 
 Tell the user (omit the obsidian line unless --obsidian was given; omit the wiki line unless --wiki was given):
diff --git a/graphify/skill-droid.md b/graphify/skill-droid.md
index fd148d485..dd09cc4a8 100644
--- a/graphify/skill-droid.md
+++ b/graphify/skill-droid.md
@@ -617,7 +617,7 @@ print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_t
 "
 rm -f graphify-out/.graphify_detect.json graphify-out/.graphify_extract.json graphify-out/.graphify_ast.json graphify-out/.graphify_semantic.json graphify-out/.graphify_analysis.json
 find graphify-out -maxdepth 1 -name '.graphify_chunk_*.json' -delete 2>/dev/null
-rm -f graphify-out/.needs_update 2>/dev/null || true
+rm -f graphify-out/needs_update 2>/dev/null || true
 ```
 
 Replace INPUT_PATH with the actual path (same value used in Steps 4-5) so the manifest is relativized to the scan root.
diff --git a/graphify/skill-kilo.md b/graphify/skill-kilo.md
index 3e70b050a..27b345a4b 100644
--- a/graphify/skill-kilo.md
+++ b/graphify/skill-kilo.md
@@ -620,7 +620,7 @@ print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_t
 "
 rm -f graphify-out/.graphify_detect.json graphify-out/.graphify_extract.json graphify-out/.graphify_ast.json graphify-out/.graphify_semantic.json graphify-out/.graphify_analysis.json
 find graphify-out -maxdepth 1 -name '.graphify_chunk_*.json' -delete 2>/dev/null
-rm -f graphify-out/.needs_update 2>/dev/null || true
+rm -f graphify-out/needs_update 2>/dev/null || true
 ```
 
 Replace INPUT_PATH with the actual path (same value used in Steps 4-5) so the manifest is relativized to the scan root.
diff --git a/graphify/skill-kiro.md b/graphify/skill-kiro.md
index abd2811d2..a65de35b4 100644
--- a/graphify/skill-kiro.md
+++ b/graphify/skill-kiro.md
@@ -620,7 +620,7 @@ print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_t
 "
 rm -f graphify-out/.graphify_detect.json graphify-out/.graphify_extract.json graphify-out/.graphify_ast.json graphify-out/.graphify_semantic.json graphify-out/.graphify_analysis.json
 find graphify-out -maxdepth 1 -name '.graphify_chunk_*.json' -delete 2>/dev/null
-rm -f graphify-out/.needs_update 2>/dev/null || true
+rm -f graphify-out/needs_update 2>/dev/null || true
 ```
 
 Replace INPUT_PATH with the actual path (same value used in Steps 4-5) so the manifest is relativized to the scan root.
diff --git a/graphify/skill-opencode.md b/graphify/skill-opencode.md
index 91ced6067..0ce2b83d6 100644
--- a/graphify/skill-opencode.md
+++ b/graphify/skill-opencode.md
@@ -612,7 +612,7 @@ print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_t
 "
 rm -f graphify-out/.graphify_detect.json graphify-out/.graphify_extract.json graphify-out/.graphify_ast.json graphify-out/.graphify_semantic.json graphify-out/.graphify_analysis.json
 find graphify-out -maxdepth 1 -name '.graphify_chunk_*.json' -delete 2>/dev/null
-rm -f graphify-out/.needs_update 2>/dev/null || true
+rm -f graphify-out/needs_update 2>/dev/null || true
 ```
 
 Replace INPUT_PATH with the actual path (same value used in Steps 4-5) so the manifest is relativized to the scan root.
diff --git a/graphify/skill-pi.md b/graphify/skill-pi.md
index abd2811d2..a65de35b4 100644
--- a/graphify/skill-pi.md
+++ b/graphify/skill-pi.md
@@ -620,7 +620,7 @@ print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_t
 "
 rm -f graphify-out/.graphify_detect.json graphify-out/.graphify_extract.json graphify-out/.graphify_ast.json graphify-out/.graphify_semantic.json graphify-out/.graphify_analysis.json
 find graphify-out -maxdepth 1 -name '.graphify_chunk_*.json' -delete 2>/dev/null
-rm -f graphify-out/.needs_update 2>/dev/null || true
+rm -f graphify-out/needs_update 2>/dev/null || true
 ```
 
 Replace INPUT_PATH with the actual path (same value used in Steps 4-5) so the manifest is relativized to the scan root.
diff --git a/graphify/skill-trae.md b/graphify/skill-trae.md
index 050667bc2..2d118ed5c 100644
--- a/graphify/skill-trae.md
+++ b/graphify/skill-trae.md
@@ -618,7 +618,7 @@ print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_t
 "
 rm -f graphify-out/.graphify_detect.json graphify-out/.graphify_extract.json graphify-out/.graphify_ast.json graphify-out/.graphify_semantic.json graphify-out/.graphify_analysis.json
 find graphify-out -maxdepth 1 -name '.graphify_chunk_*.json' -delete 2>/dev/null
-rm -f graphify-out/.needs_update 2>/dev/null || true
+rm -f graphify-out/needs_update 2>/dev/null || true
 ```
 
 Replace INPUT_PATH with the actual path (same value used in Steps 4-5) so the manifest is relativized to the scan root.
diff --git a/graphify/skill-vscode.md b/graphify/skill-vscode.md
index 20c7c0835..4dc11750f 100644
--- a/graphify/skill-vscode.md
+++ b/graphify/skill-vscode.md
@@ -616,7 +616,7 @@ print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_t
 "
 rm -f graphify-out/.graphify_detect.json graphify-out/.graphify_extract.json graphify-out/.graphify_ast.json graphify-out/.graphify_semantic.json graphify-out/.graphify_analysis.json
 find graphify-out -maxdepth 1 -name '.graphify_chunk_*.json' -delete 2>/dev/null
-rm -f graphify-out/.needs_update 2>/dev/null || true
+rm -f graphify-out/needs_update 2>/dev/null || true
 ```
 
 Replace INPUT_PATH with the actual path (same value used in Steps 4-5) so the manifest is relativized to the scan root.
diff --git a/graphify/skill-windows.md b/graphify/skill-windows.md
index d631821ec..eb17a6a34 100644
--- a/graphify/skill-windows.md
+++ b/graphify/skill-windows.md
@@ -642,7 +642,7 @@ print(f'All time: {cost["total_input_tokens"]:,} input, {cost["total_output_toke
 '@ | & (Get-Content graphify-out\.graphify_python) -
 Remove-Item -Force -ErrorAction SilentlyContinue graphify-out\.graphify_detect.json, graphify-out\.graphify_extract.json, graphify-out\.graphify_ast.json, graphify-out\.graphify_semantic.json, graphify-out\.graphify_analysis.json
 Get-ChildItem graphify-out -Filter '.graphify_chunk_*.json' -File -ErrorAction SilentlyContinue | Remove-Item -Force
-Remove-Item -Force -ErrorAction SilentlyContinue graphify-out\.needs_update
+Remove-Item -Force -ErrorAction SilentlyContinue graphify-out\needs_update
 ```
 
 Replace INPUT_PATH with the actual path (same value used in Steps 4-5) so the manifest is relativized to the scan root.
diff --git a/graphify/skill.md b/graphify/skill.md
index abd2811d2..a65de35b4 100644
--- a/graphify/skill.md
+++ b/graphify/skill.md
@@ -620,7 +620,7 @@ print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_t
 "
 rm -f graphify-out/.graphify_detect.json graphify-out/.graphify_extract.json graphify-out/.graphify_ast.json graphify-out/.graphify_semantic.json graphify-out/.graphify_analysis.json
 find graphify-out -maxdepth 1 -name '.graphify_chunk_*.json' -delete 2>/dev/null
-rm -f graphify-out/.needs_update 2>/dev/null || true
+rm -f graphify-out/needs_update 2>/dev/null || true
 ```
 
 Replace INPUT_PATH with the actual path (same value used in Steps 4-5) so the manifest is relativized to the scan root.
diff --git a/tools/skillgen/expected/graphify__skill-agents.md b/tools/skillgen/expected/graphify__skill-agents.md
index 190827d9a..d3d4a2869 100644
--- a/tools/skillgen/expected/graphify__skill-agents.md
+++ b/tools/skillgen/expected/graphify__skill-agents.md
@@ -617,7 +617,7 @@ print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_t
 "
 rm -f graphify-out/.graphify_detect.json graphify-out/.graphify_extract.json graphify-out/.graphify_ast.json graphify-out/.graphify_semantic.json graphify-out/.graphify_analysis.json
 find graphify-out -maxdepth 1 -name '.graphify_chunk_*.json' -delete 2>/dev/null
-rm -f graphify-out/.needs_update 2>/dev/null || true
+rm -f graphify-out/needs_update 2>/dev/null || true
 ```
 
 Replace INPUT_PATH with the actual path (same value used in Steps 4-5) so the manifest is relativized to the scan root.
diff --git a/tools/skillgen/expected/graphify__skill-aider.md b/tools/skillgen/expected/graphify__skill-aider.md
index 4996beb78..d0c308b8f 100644
--- a/tools/skillgen/expected/graphify__skill-aider.md
+++ b/tools/skillgen/expected/graphify__skill-aider.md
@@ -720,7 +720,7 @@ print(f'This run: {input_tok:,} input tokens, {output_tok:,} output tokens')
 print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_tokens\"]:,} output ({len(cost[\"runs\"])} runs)')
 "
 rm -f .graphify_detect.json .graphify_extract.json .graphify_ast.json .graphify_semantic.json .graphify_analysis.json .graphify_labels.json; find . -maxdepth 1 -name '.graphify_chunk_*.json' -delete 2>/dev/null
-rm -f graphify-out/.needs_update 2>/dev/null || true
+rm -f graphify-out/needs_update 2>/dev/null || true
 ```
 
 Tell the user (omit the obsidian line unless --obsidian was given):
diff --git a/tools/skillgen/expected/graphify__skill-amp.md b/tools/skillgen/expected/graphify__skill-amp.md
index 190827d9a..d3d4a2869 100644
--- a/tools/skillgen/expected/graphify__skill-amp.md
+++ b/tools/skillgen/expected/graphify__skill-amp.md
@@ -617,7 +617,7 @@ print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_t
 "
 rm -f graphify-out/.graphify_detect.json graphify-out/.graphify_extract.json graphify-out/.graphify_ast.json graphify-out/.graphify_semantic.json graphify-out/.graphify_analysis.json
 find graphify-out -maxdepth 1 -name '.graphify_chunk_*.json' -delete 2>/dev/null
-rm -f graphify-out/.needs_update 2>/dev/null || true
+rm -f graphify-out/needs_update 2>/dev/null || true
 ```
 
 Replace INPUT_PATH with the actual path (same value used in Steps 4-5) so the manifest is relativized to the scan root.
diff --git a/tools/skillgen/expected/graphify__skill-claw.md b/tools/skillgen/expected/graphify__skill-claw.md
index abd2811d2..a65de35b4 100644
--- a/tools/skillgen/expected/graphify__skill-claw.md
+++ b/tools/skillgen/expected/graphify__skill-claw.md
@@ -620,7 +620,7 @@ print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_t
 "
 rm -f graphify-out/.graphify_detect.json graphify-out/.graphify_extract.json graphify-out/.graphify_ast.json graphify-out/.graphify_semantic.json graphify-out/.graphify_analysis.json
 find graphify-out -maxdepth 1 -name '.graphify_chunk_*.json' -delete 2>/dev/null
-rm -f graphify-out/.needs_update 2>/dev/null || true
+rm -f graphify-out/needs_update 2>/dev/null || true
 ```
 
 Replace INPUT_PATH with the actual path (same value used in Steps 4-5) so the manifest is relativized to the scan root.
diff --git a/tools/skillgen/expected/graphify__skill-codex.md b/tools/skillgen/expected/graphify__skill-codex.md
index af3f723c7..42e0bd473 100644
--- a/tools/skillgen/expected/graphify__skill-codex.md
+++ b/tools/skillgen/expected/graphify__skill-codex.md
@@ -617,7 +617,7 @@ print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_t
 "
 rm -f graphify-out/.graphify_detect.json graphify-out/.graphify_extract.json graphify-out/.graphify_ast.json graphify-out/.graphify_semantic.json graphify-out/.graphify_analysis.json
 find graphify-out -maxdepth 1 -name '.graphify_chunk_*.json' -delete 2>/dev/null
-rm -f graphify-out/.needs_update 2>/dev/null || true
+rm -f graphify-out/needs_update 2>/dev/null || true
 ```
 
 Replace INPUT_PATH with the actual path (same value used in Steps 4-5) so the manifest is relativized to the scan root.
diff --git a/tools/skillgen/expected/graphify__skill-copilot.md b/tools/skillgen/expected/graphify__skill-copilot.md
index abd2811d2..a65de35b4 100644
--- a/tools/skillgen/expected/graphify__skill-copilot.md
+++ b/tools/skillgen/expected/graphify__skill-copilot.md
@@ -620,7 +620,7 @@ print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_t
 "
 rm -f graphify-out/.graphify_detect.json graphify-out/.graphify_extract.json graphify-out/.graphify_ast.json graphify-out/.graphify_semantic.json graphify-out/.graphify_analysis.json
 find graphify-out -maxdepth 1 -name '.graphify_chunk_*.json' -delete 2>/dev/null
-rm -f graphify-out/.needs_update 2>/dev/null || true
+rm -f graphify-out/needs_update 2>/dev/null || true
 ```
 
 Replace INPUT_PATH with the actual path (same value used in Steps 4-5) so the manifest is relativized to the scan root.
diff --git a/tools/skillgen/expected/graphify__skill-devin.md b/tools/skillgen/expected/graphify__skill-devin.md
index f9be846cb..5d720b633 100644
--- a/tools/skillgen/expected/graphify__skill-devin.md
+++ b/tools/skillgen/expected/graphify__skill-devin.md
@@ -838,7 +838,7 @@ print(f'This run: {input_tok:,} input tokens, {output_tok:,} output tokens')
 print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_tokens\"]:,} output ({len(cost[\"runs\"])} runs)')
 "
 rm -f graphify-out/.graphify_detect.json graphify-out/.graphify_extract.json graphify-out/.graphify_ast.json graphify-out/.graphify_semantic.json graphify-out/.graphify_analysis.json graphify-out/.graphify_labels.json graphify-out/.graphify_incremental.json graphify-out/.graphify_transcripts.json graphify-out/.graphify_old.json; find graphify-out -maxdepth 1 -name '.graphify_chunk_*.json' -delete 2>/dev/null
-rm -f graphify-out/.needs_update 2>/dev/null || true
+rm -f graphify-out/needs_update 2>/dev/null || true
 ```
 
 Tell the user (omit the obsidian line unless --obsidian was given; omit the wiki line unless --wiki was given):
diff --git a/tools/skillgen/expected/graphify__skill-droid.md b/tools/skillgen/expected/graphify__skill-droid.md
index fd148d485..dd09cc4a8 100644
--- a/tools/skillgen/expected/graphify__skill-droid.md
+++ b/tools/skillgen/expected/graphify__skill-droid.md
@@ -617,7 +617,7 @@ print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_t
 "
 rm -f graphify-out/.graphify_detect.json graphify-out/.graphify_extract.json graphify-out/.graphify_ast.json graphify-out/.graphify_semantic.json graphify-out/.graphify_analysis.json
 find graphify-out -maxdepth 1 -name '.graphify_chunk_*.json' -delete 2>/dev/null
-rm -f graphify-out/.needs_update 2>/dev/null || true
+rm -f graphify-out/needs_update 2>/dev/null || true
 ```
 
 Replace INPUT_PATH with the actual path (same value used in Steps 4-5) so the manifest is relativized to the scan root.
diff --git a/tools/skillgen/expected/graphify__skill-kilo.md b/tools/skillgen/expected/graphify__skill-kilo.md
index 3e70b050a..27b345a4b 100644
--- a/tools/skillgen/expected/graphify__skill-kilo.md
+++ b/tools/skillgen/expected/graphify__skill-kilo.md
@@ -620,7 +620,7 @@ print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_t
 "
 rm -f graphify-out/.graphify_detect.json graphify-out/.graphify_extract.json graphify-out/.graphify_ast.json graphify-out/.graphify_semantic.json graphify-out/.graphify_analysis.json
 find graphify-out -maxdepth 1 -name '.graphify_chunk_*.json' -delete 2>/dev/null
-rm -f graphify-out/.needs_update 2>/dev/null || true
+rm -f graphify-out/needs_update 2>/dev/null || true
 ```
 
 Replace INPUT_PATH with the actual path (same value used in Steps 4-5) so the manifest is relativized to the scan root.
diff --git a/tools/skillgen/expected/graphify__skill-kiro.md b/tools/skillgen/expected/graphify__skill-kiro.md
index abd2811d2..a65de35b4 100644
--- a/tools/skillgen/expected/graphify__skill-kiro.md
+++ b/tools/skillgen/expected/graphify__skill-kiro.md
@@ -620,7 +620,7 @@ print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_t
 "
 rm -f graphify-out/.graphify_detect.json graphify-out/.graphify_extract.json graphify-out/.graphify_ast.json graphify-out/.graphify_semantic.json graphify-out/.graphify_analysis.json
 find graphify-out -maxdepth 1 -name '.graphify_chunk_*.json' -delete 2>/dev/null
-rm -f graphify-out/.needs_update 2>/dev/null || true
+rm -f graphify-out/needs_update 2>/dev/null || true
 ```
 
 Replace INPUT_PATH with the actual path (same value used in Steps 4-5) so the manifest is relativized to the scan root.
diff --git a/tools/skillgen/expected/graphify__skill-opencode.md b/tools/skillgen/expected/graphify__skill-opencode.md
index 91ced6067..0ce2b83d6 100644
--- a/tools/skillgen/expected/graphify__skill-opencode.md
+++ b/tools/skillgen/expected/graphify__skill-opencode.md
@@ -612,7 +612,7 @@ print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_t
 "
 rm -f graphify-out/.graphify_detect.json graphify-out/.graphify_extract.json graphify-out/.graphify_ast.json graphify-out/.graphify_semantic.json graphify-out/.graphify_analysis.json
 find graphify-out -maxdepth 1 -name '.graphify_chunk_*.json' -delete 2>/dev/null
-rm -f graphify-out/.needs_update 2>/dev/null || true
+rm -f graphify-out/needs_update 2>/dev/null || true
 ```
 
 Replace INPUT_PATH with the actual path (same value used in Steps 4-5) so the manifest is relativized to the scan root.
diff --git a/tools/skillgen/expected/graphify__skill-pi.md b/tools/skillgen/expected/graphify__skill-pi.md
index abd2811d2..a65de35b4 100644
--- a/tools/skillgen/expected/graphify__skill-pi.md
+++ b/tools/skillgen/expected/graphify__skill-pi.md
@@ -620,7 +620,7 @@ print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_t
 "
 rm -f graphify-out/.graphify_detect.json graphify-out/.graphify_extract.json graphify-out/.graphify_ast.json graphify-out/.graphify_semantic.json graphify-out/.graphify_analysis.json
 find graphify-out -maxdepth 1 -name '.graphify_chunk_*.json' -delete 2>/dev/null
-rm -f graphify-out/.needs_update 2>/dev/null || true
+rm -f graphify-out/needs_update 2>/dev/null || true
 ```
 
 Replace INPUT_PATH with the actual path (same value used in Steps 4-5) so the manifest is relativized to the scan root.
diff --git a/tools/skillgen/expected/graphify__skill-trae.md b/tools/skillgen/expected/graphify__skill-trae.md
index 050667bc2..2d118ed5c 100644
--- a/tools/skillgen/expected/graphify__skill-trae.md
+++ b/tools/skillgen/expected/graphify__skill-trae.md
@@ -618,7 +618,7 @@ print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_t
 "
 rm -f graphify-out/.graphify_detect.json graphify-out/.graphify_extract.json graphify-out/.graphify_ast.json graphify-out/.graphify_semantic.json graphify-out/.graphify_analysis.json
 find graphify-out -maxdepth 1 -name '.graphify_chunk_*.json' -delete 2>/dev/null
-rm -f graphify-out/.needs_update 2>/dev/null || true
+rm -f graphify-out/needs_update 2>/dev/null || true
 ```
 
 Replace INPUT_PATH with the actual path (same value used in Steps 4-5) so the manifest is relativized to the scan root.
diff --git a/tools/skillgen/expected/graphify__skill-vscode.md b/tools/skillgen/expected/graphify__skill-vscode.md
index 20c7c0835..4dc11750f 100644
--- a/tools/skillgen/expected/graphify__skill-vscode.md
+++ b/tools/skillgen/expected/graphify__skill-vscode.md
@@ -616,7 +616,7 @@ print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_t
 "
 rm -f graphify-out/.graphify_detect.json graphify-out/.graphify_extract.json graphify-out/.graphify_ast.json graphify-out/.graphify_semantic.json graphify-out/.graphify_analysis.json
 find graphify-out -maxdepth 1 -name '.graphify_chunk_*.json' -delete 2>/dev/null
-rm -f graphify-out/.needs_update 2>/dev/null || true
+rm -f graphify-out/needs_update 2>/dev/null || true
 ```
 
 Replace INPUT_PATH with the actual path (same value used in Steps 4-5) so the manifest is relativized to the scan root.
diff --git a/tools/skillgen/expected/graphify__skill-windows.md b/tools/skillgen/expected/graphify__skill-windows.md
index d631821ec..eb17a6a34 100644
--- a/tools/skillgen/expected/graphify__skill-windows.md
+++ b/tools/skillgen/expected/graphify__skill-windows.md
@@ -642,7 +642,7 @@ print(f'All time: {cost["total_input_tokens"]:,} input, {cost["total_output_toke
 '@ | & (Get-Content graphify-out\.graphify_python) -
 Remove-Item -Force -ErrorAction SilentlyContinue graphify-out\.graphify_detect.json, graphify-out\.graphify_extract.json, graphify-out\.graphify_ast.json, graphify-out\.graphify_semantic.json, graphify-out\.graphify_analysis.json
 Get-ChildItem graphify-out -Filter '.graphify_chunk_*.json' -File -ErrorAction SilentlyContinue | Remove-Item -Force
-Remove-Item -Force -ErrorAction SilentlyContinue graphify-out\.needs_update
+Remove-Item -Force -ErrorAction SilentlyContinue graphify-out\needs_update
 ```
 
 Replace INPUT_PATH with the actual path (same value used in Steps 4-5) so the manifest is relativized to the scan root.
diff --git a/tools/skillgen/expected/graphify__skill.md b/tools/skillgen/expected/graphify__skill.md
index abd2811d2..a65de35b4 100644
--- a/tools/skillgen/expected/graphify__skill.md
+++ b/tools/skillgen/expected/graphify__skill.md
@@ -620,7 +620,7 @@ print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_t
 "
 rm -f graphify-out/.graphify_detect.json graphify-out/.graphify_extract.json graphify-out/.graphify_ast.json graphify-out/.graphify_semantic.json graphify-out/.graphify_analysis.json
 find graphify-out -maxdepth 1 -name '.graphify_chunk_*.json' -delete 2>/dev/null
-rm -f graphify-out/.needs_update 2>/dev/null || true
+rm -f graphify-out/needs_update 2>/dev/null || true
 ```
 
 Replace INPUT_PATH with the actual path (same value used in Steps 4-5) so the manifest is relativized to the scan root.
diff --git a/tools/skillgen/fragments/core/aider.md b/tools/skillgen/fragments/core/aider.md
index 4996beb78..d0c308b8f 100644
--- a/tools/skillgen/fragments/core/aider.md
+++ b/tools/skillgen/fragments/core/aider.md
@@ -720,7 +720,7 @@ print(f'This run: {input_tok:,} input tokens, {output_tok:,} output tokens')
 print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_tokens\"]:,} output ({len(cost[\"runs\"])} runs)')
 "
 rm -f .graphify_detect.json .graphify_extract.json .graphify_ast.json .graphify_semantic.json .graphify_analysis.json .graphify_labels.json; find . -maxdepth 1 -name '.graphify_chunk_*.json' -delete 2>/dev/null
-rm -f graphify-out/.needs_update 2>/dev/null || true
+rm -f graphify-out/needs_update 2>/dev/null || true
 ```
 
 Tell the user (omit the obsidian line unless --obsidian was given):
diff --git a/tools/skillgen/fragments/core/core.md b/tools/skillgen/fragments/core/core.md
index c527a1256..d73b50c15 100644
--- a/tools/skillgen/fragments/core/core.md
+++ b/tools/skillgen/fragments/core/core.md
@@ -555,7 +555,7 @@ print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_t
 "
 rm -f graphify-out/.graphify_detect.json graphify-out/.graphify_extract.json graphify-out/.graphify_ast.json graphify-out/.graphify_semantic.json graphify-out/.graphify_analysis.json
 find graphify-out -maxdepth 1 -name '.graphify_chunk_*.json' -delete 2>/dev/null
-rm -f graphify-out/.needs_update 2>/dev/null || true
+rm -f graphify-out/needs_update 2>/dev/null || true
 ```
 
 Replace INPUT_PATH with the actual path (same value used in Steps 4-5) so the manifest is relativized to the scan root.
diff --git a/tools/skillgen/fragments/core/devin.md b/tools/skillgen/fragments/core/devin.md
index f9be846cb..5d720b633 100644
--- a/tools/skillgen/fragments/core/devin.md
+++ b/tools/skillgen/fragments/core/devin.md
@@ -838,7 +838,7 @@ print(f'This run: {input_tok:,} input tokens, {output_tok:,} output tokens')
 print(f'All time: {cost[\"total_input_tokens\"]:,} input, {cost[\"total_output_tokens\"]:,} output ({len(cost[\"runs\"])} runs)')
 "
 rm -f graphify-out/.graphify_detect.json graphify-out/.graphify_extract.json graphify-out/.graphify_ast.json graphify-out/.graphify_semantic.json graphify-out/.graphify_analysis.json graphify-out/.graphify_labels.json graphify-out/.graphify_incremental.json graphify-out/.graphify_transcripts.json graphify-out/.graphify_old.json; find graphify-out -maxdepth 1 -name '.graphify_chunk_*.json' -delete 2>/dev/null
-rm -f graphify-out/.needs_update 2>/dev/null || true
+rm -f graphify-out/needs_update 2>/dev/null || true
 ```
 
 Tell the user (omit the obsidian line unless --obsidian was given; omit the wiki line unless --wiki was given):
diff --git a/tools/skillgen/gen.py b/tools/skillgen/gen.py
index 09e19ede0..e4d3b3fb1 100644
--- a/tools/skillgen/gen.py
+++ b/tools/skillgen/gen.py
@@ -1142,6 +1142,22 @@ def _is_community_label_export_fix_line(line: str) -> bool:
     )
 
 
+def _is_needs_update_dot_fix_line(line: str) -> bool:
+    """Whether a line is the ``needs_update`` dot-mismatch fix (#2671).
+
+    The cleanup step's ``rm -f`` targeted ``graphify-out/.needs_update`` (with a
+    leading dot), but every writer/reader of the flag — ``watch.py``'s
+    ``needs_update`` path and ``cli.py``'s ``out_path("needs_update")`` check —
+    uses the name WITHOUT a dot. So the cleanup line never matched the real
+    file and any staleness check an agent wrote against the documented
+    (dotted) name silently never fired. Both the old (removed) and new
+    (added) forms of the single ``rm -f`` line match here.
+    """
+    return "rm -f graphify-out/" in line and line.rstrip().endswith(
+        "needs_update 2>/dev/null || true"
+    )
+
+
 # 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
@@ -1163,6 +1179,7 @@ def _is_community_label_export_fix_line(line: str) -> bool:
     _is_uv_from_interpreter_fix_line,
     _is_semantic_cache_scope_fix_line,
     _is_community_label_export_fix_line,
+    _is_needs_update_dot_fix_line,
 )