diff --git a/graphify/skill-agents.md b/graphify/skill-agents.md
index 190827d9ac..c14e438a30 100644
--- a/graphify/skill-agents.md
+++ b/graphify/skill-agents.md
@@ -97,7 +97,7 @@ fi
 mkdir -p graphify-out
 "$PYTHON" -c "import sys; open('graphify-out/.graphify_python', 'w', encoding='utf-8').write(sys.executable)"
 # Save scan root so `graphify update` (no args) knows where to look next time
-echo "$(cd INPUT_PATH && pwd)" > graphify-out/.graphify_root
+echo "$(cd "INPUT_PATH" && pwd)" > graphify-out/.graphify_root
 ```
 
 If the import succeeds, print nothing and move straight to Step 2.
@@ -176,7 +176,6 @@ $(cat graphify-out/.graphify_python) -c "
 import sys, json
 from graphify.extract import collect_files, extract
 from pathlib import Path
-import json
 
 code_files = []
 detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encoding=\"utf-8\"))
@@ -542,7 +541,6 @@ Generate the HTML graph (always, unless `--no-viz`):
 
 ```bash
 graphify export html  # auto-aggregates to community view if graph > 5000 nodes
-# or: graphify export html --no-viz
 ```
 
 ### Steps 6b-8 - Wiki, Neo4j, FalkorDB, SVG, GraphML, MCP, benchmark (only on their flags)
diff --git a/graphify/skill-amp.md b/graphify/skill-amp.md
index 190827d9ac..c14e438a30 100644
--- a/graphify/skill-amp.md
+++ b/graphify/skill-amp.md
@@ -97,7 +97,7 @@ fi
 mkdir -p graphify-out
 "$PYTHON" -c "import sys; open('graphify-out/.graphify_python', 'w', encoding='utf-8').write(sys.executable)"
 # Save scan root so `graphify update` (no args) knows where to look next time
-echo "$(cd INPUT_PATH && pwd)" > graphify-out/.graphify_root
+echo "$(cd "INPUT_PATH" && pwd)" > graphify-out/.graphify_root
 ```
 
 If the import succeeds, print nothing and move straight to Step 2.
@@ -176,7 +176,6 @@ $(cat graphify-out/.graphify_python) -c "
 import sys, json
 from graphify.extract import collect_files, extract
 from pathlib import Path
-import json
 
 code_files = []
 detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encoding=\"utf-8\"))
@@ -542,7 +541,6 @@ Generate the HTML graph (always, unless `--no-viz`):
 
 ```bash
 graphify export html  # auto-aggregates to community view if graph > 5000 nodes
-# or: graphify export html --no-viz
 ```
 
 ### Steps 6b-8 - Wiki, Neo4j, FalkorDB, SVG, GraphML, MCP, benchmark (only on their flags)
diff --git a/graphify/skill-claw.md b/graphify/skill-claw.md
index abd2811d23..65bb2ec32d 100644
--- a/graphify/skill-claw.md
+++ b/graphify/skill-claw.md
@@ -97,7 +97,7 @@ fi
 mkdir -p graphify-out
 "$PYTHON" -c "import sys; open('graphify-out/.graphify_python', 'w', encoding='utf-8').write(sys.executable)"
 # Save scan root so `graphify update` (no args) knows where to look next time
-echo "$(cd INPUT_PATH && pwd)" > graphify-out/.graphify_root
+echo "$(cd "INPUT_PATH" && pwd)" > graphify-out/.graphify_root
 ```
 
 If the import succeeds, print nothing and move straight to Step 2.
@@ -176,7 +176,6 @@ $(cat graphify-out/.graphify_python) -c "
 import sys, json
 from graphify.extract import collect_files, extract
 from pathlib import Path
-import json
 
 code_files = []
 detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encoding=\"utf-8\"))
@@ -545,7 +544,6 @@ Generate the HTML graph (always, unless `--no-viz`):
 
 ```bash
 graphify export html  # auto-aggregates to community view if graph > 5000 nodes
-# or: graphify export html --no-viz
 ```
 
 ### Steps 6b-8 - Wiki, Neo4j, FalkorDB, SVG, GraphML, MCP, benchmark (only on their flags)
diff --git a/graphify/skill-codex.md b/graphify/skill-codex.md
index af3f723c78..2bf76c2d76 100644
--- a/graphify/skill-codex.md
+++ b/graphify/skill-codex.md
@@ -97,7 +97,7 @@ fi
 mkdir -p graphify-out
 "$PYTHON" -c "import sys; open('graphify-out/.graphify_python', 'w', encoding='utf-8').write(sys.executable)"
 # Save scan root so `graphify update` (no args) knows where to look next time
-echo "$(cd INPUT_PATH && pwd)" > graphify-out/.graphify_root
+echo "$(cd "INPUT_PATH" && pwd)" > graphify-out/.graphify_root
 ```
 
 If the import succeeds, print nothing and move straight to Step 2.
@@ -176,7 +176,6 @@ $(cat graphify-out/.graphify_python) -c "
 import sys, json
 from graphify.extract import collect_files, extract
 from pathlib import Path
-import json
 
 code_files = []
 detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encoding=\"utf-8\"))
@@ -542,7 +541,6 @@ Generate the HTML graph (always, unless `--no-viz`):
 
 ```bash
 graphify export html  # auto-aggregates to community view if graph > 5000 nodes
-# or: graphify export html --no-viz
 ```
 
 ### Steps 6b-8 - Wiki, Neo4j, FalkorDB, SVG, GraphML, MCP, benchmark (only on their flags)
diff --git a/graphify/skill-copilot.md b/graphify/skill-copilot.md
index abd2811d23..65bb2ec32d 100644
--- a/graphify/skill-copilot.md
+++ b/graphify/skill-copilot.md
@@ -97,7 +97,7 @@ fi
 mkdir -p graphify-out
 "$PYTHON" -c "import sys; open('graphify-out/.graphify_python', 'w', encoding='utf-8').write(sys.executable)"
 # Save scan root so `graphify update` (no args) knows where to look next time
-echo "$(cd INPUT_PATH && pwd)" > graphify-out/.graphify_root
+echo "$(cd "INPUT_PATH" && pwd)" > graphify-out/.graphify_root
 ```
 
 If the import succeeds, print nothing and move straight to Step 2.
@@ -176,7 +176,6 @@ $(cat graphify-out/.graphify_python) -c "
 import sys, json
 from graphify.extract import collect_files, extract
 from pathlib import Path
-import json
 
 code_files = []
 detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encoding=\"utf-8\"))
@@ -545,7 +544,6 @@ Generate the HTML graph (always, unless `--no-viz`):
 
 ```bash
 graphify export html  # auto-aggregates to community view if graph > 5000 nodes
-# or: graphify export html --no-viz
 ```
 
 ### Steps 6b-8 - Wiki, Neo4j, FalkorDB, SVG, GraphML, MCP, benchmark (only on their flags)
diff --git a/graphify/skill-droid.md b/graphify/skill-droid.md
index fd148d485d..0353795e9e 100644
--- a/graphify/skill-droid.md
+++ b/graphify/skill-droid.md
@@ -97,7 +97,7 @@ fi
 mkdir -p graphify-out
 "$PYTHON" -c "import sys; open('graphify-out/.graphify_python', 'w', encoding='utf-8').write(sys.executable)"
 # Save scan root so `graphify update` (no args) knows where to look next time
-echo "$(cd INPUT_PATH && pwd)" > graphify-out/.graphify_root
+echo "$(cd "INPUT_PATH" && pwd)" > graphify-out/.graphify_root
 ```
 
 If the import succeeds, print nothing and move straight to Step 2.
@@ -176,7 +176,6 @@ $(cat graphify-out/.graphify_python) -c "
 import sys, json
 from graphify.extract import collect_files, extract
 from pathlib import Path
-import json
 
 code_files = []
 detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encoding=\"utf-8\"))
@@ -542,7 +541,6 @@ Generate the HTML graph (always, unless `--no-viz`):
 
 ```bash
 graphify export html  # auto-aggregates to community view if graph > 5000 nodes
-# or: graphify export html --no-viz
 ```
 
 ### Steps 6b-8 - Wiki, Neo4j, FalkorDB, SVG, GraphML, MCP, benchmark (only on their flags)
diff --git a/graphify/skill-kilo.md b/graphify/skill-kilo.md
index 3e70b050a4..0e38970de0 100644
--- a/graphify/skill-kilo.md
+++ b/graphify/skill-kilo.md
@@ -97,7 +97,7 @@ fi
 mkdir -p graphify-out
 "$PYTHON" -c "import sys; open('graphify-out/.graphify_python', 'w', encoding='utf-8').write(sys.executable)"
 # Save scan root so `graphify update` (no args) knows where to look next time
-echo "$(cd INPUT_PATH && pwd)" > graphify-out/.graphify_root
+echo "$(cd "INPUT_PATH" && pwd)" > graphify-out/.graphify_root
 ```
 
 If the import succeeds, print nothing and move straight to Step 2.
@@ -176,7 +176,6 @@ $(cat graphify-out/.graphify_python) -c "
 import sys, json
 from graphify.extract import collect_files, extract
 from pathlib import Path
-import json
 
 code_files = []
 detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encoding=\"utf-8\"))
@@ -545,7 +544,6 @@ Generate the HTML graph (always, unless `--no-viz`):
 
 ```bash
 graphify export html  # auto-aggregates to community view if graph > 5000 nodes
-# or: graphify export html --no-viz
 ```
 
 ### Steps 6b-8 - Wiki, Neo4j, FalkorDB, SVG, GraphML, MCP, benchmark (only on their flags)
diff --git a/graphify/skill-kiro.md b/graphify/skill-kiro.md
index abd2811d23..65bb2ec32d 100644
--- a/graphify/skill-kiro.md
+++ b/graphify/skill-kiro.md
@@ -97,7 +97,7 @@ fi
 mkdir -p graphify-out
 "$PYTHON" -c "import sys; open('graphify-out/.graphify_python', 'w', encoding='utf-8').write(sys.executable)"
 # Save scan root so `graphify update` (no args) knows where to look next time
-echo "$(cd INPUT_PATH && pwd)" > graphify-out/.graphify_root
+echo "$(cd "INPUT_PATH" && pwd)" > graphify-out/.graphify_root
 ```
 
 If the import succeeds, print nothing and move straight to Step 2.
@@ -176,7 +176,6 @@ $(cat graphify-out/.graphify_python) -c "
 import sys, json
 from graphify.extract import collect_files, extract
 from pathlib import Path
-import json
 
 code_files = []
 detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encoding=\"utf-8\"))
@@ -545,7 +544,6 @@ Generate the HTML graph (always, unless `--no-viz`):
 
 ```bash
 graphify export html  # auto-aggregates to community view if graph > 5000 nodes
-# or: graphify export html --no-viz
 ```
 
 ### Steps 6b-8 - Wiki, Neo4j, FalkorDB, SVG, GraphML, MCP, benchmark (only on their flags)
diff --git a/graphify/skill-opencode.md b/graphify/skill-opencode.md
index 91ced60675..0022c7a243 100644
--- a/graphify/skill-opencode.md
+++ b/graphify/skill-opencode.md
@@ -97,7 +97,7 @@ fi
 mkdir -p graphify-out
 "$PYTHON" -c "import sys; open('graphify-out/.graphify_python', 'w', encoding='utf-8').write(sys.executable)"
 # Save scan root so `graphify update` (no args) knows where to look next time
-echo "$(cd INPUT_PATH && pwd)" > graphify-out/.graphify_root
+echo "$(cd "INPUT_PATH" && pwd)" > graphify-out/.graphify_root
 ```
 
 If the import succeeds, print nothing and move straight to Step 2.
@@ -176,7 +176,6 @@ $(cat graphify-out/.graphify_python) -c "
 import sys, json
 from graphify.extract import collect_files, extract
 from pathlib import Path
-import json
 
 code_files = []
 detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encoding=\"utf-8\"))
@@ -537,7 +536,6 @@ Generate the HTML graph (always, unless `--no-viz`):
 
 ```bash
 graphify export html  # auto-aggregates to community view if graph > 5000 nodes
-# or: graphify export html --no-viz
 ```
 
 ### Steps 6b-8 - Wiki, Neo4j, FalkorDB, SVG, GraphML, MCP, benchmark (only on their flags)
diff --git a/graphify/skill-pi.md b/graphify/skill-pi.md
index abd2811d23..65bb2ec32d 100644
--- a/graphify/skill-pi.md
+++ b/graphify/skill-pi.md
@@ -97,7 +97,7 @@ fi
 mkdir -p graphify-out
 "$PYTHON" -c "import sys; open('graphify-out/.graphify_python', 'w', encoding='utf-8').write(sys.executable)"
 # Save scan root so `graphify update` (no args) knows where to look next time
-echo "$(cd INPUT_PATH && pwd)" > graphify-out/.graphify_root
+echo "$(cd "INPUT_PATH" && pwd)" > graphify-out/.graphify_root
 ```
 
 If the import succeeds, print nothing and move straight to Step 2.
@@ -176,7 +176,6 @@ $(cat graphify-out/.graphify_python) -c "
 import sys, json
 from graphify.extract import collect_files, extract
 from pathlib import Path
-import json
 
 code_files = []
 detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encoding=\"utf-8\"))
@@ -545,7 +544,6 @@ Generate the HTML graph (always, unless `--no-viz`):
 
 ```bash
 graphify export html  # auto-aggregates to community view if graph > 5000 nodes
-# or: graphify export html --no-viz
 ```
 
 ### Steps 6b-8 - Wiki, Neo4j, FalkorDB, SVG, GraphML, MCP, benchmark (only on their flags)
diff --git a/graphify/skill-trae.md b/graphify/skill-trae.md
index 050667bc20..9fb9a113fb 100644
--- a/graphify/skill-trae.md
+++ b/graphify/skill-trae.md
@@ -97,7 +97,7 @@ fi
 mkdir -p graphify-out
 "$PYTHON" -c "import sys; open('graphify-out/.graphify_python', 'w', encoding='utf-8').write(sys.executable)"
 # Save scan root so `graphify update` (no args) knows where to look next time
-echo "$(cd INPUT_PATH && pwd)" > graphify-out/.graphify_root
+echo "$(cd "INPUT_PATH" && pwd)" > graphify-out/.graphify_root
 ```
 
 If the import succeeds, print nothing and move straight to Step 2.
@@ -176,7 +176,6 @@ $(cat graphify-out/.graphify_python) -c "
 import sys, json
 from graphify.extract import collect_files, extract
 from pathlib import Path
-import json
 
 code_files = []
 detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encoding=\"utf-8\"))
@@ -543,7 +542,6 @@ Generate the HTML graph (always, unless `--no-viz`):
 
 ```bash
 graphify export html  # auto-aggregates to community view if graph > 5000 nodes
-# or: graphify export html --no-viz
 ```
 
 ### Steps 6b-8 - Wiki, Neo4j, FalkorDB, SVG, GraphML, MCP, benchmark (only on their flags)
diff --git a/graphify/skill-vscode.md b/graphify/skill-vscode.md
index 20c7c0835c..310911e713 100644
--- a/graphify/skill-vscode.md
+++ b/graphify/skill-vscode.md
@@ -97,7 +97,7 @@ fi
 mkdir -p graphify-out
 "$PYTHON" -c "import sys; open('graphify-out/.graphify_python', 'w', encoding='utf-8').write(sys.executable)"
 # Save scan root so `graphify update` (no args) knows where to look next time
-echo "$(cd INPUT_PATH && pwd)" > graphify-out/.graphify_root
+echo "$(cd "INPUT_PATH" && pwd)" > graphify-out/.graphify_root
 ```
 
 If the import succeeds, print nothing and move straight to Step 2.
@@ -176,7 +176,6 @@ $(cat graphify-out/.graphify_python) -c "
 import sys, json
 from graphify.extract import collect_files, extract
 from pathlib import Path
-import json
 
 code_files = []
 detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encoding=\"utf-8\"))
@@ -541,7 +540,6 @@ Generate the HTML graph (always, unless `--no-viz`):
 
 ```bash
 graphify export html  # auto-aggregates to community view if graph > 5000 nodes
-# or: graphify export html --no-viz
 ```
 
 ### Steps 6b-8 - Wiki, Neo4j, FalkorDB, SVG, GraphML, MCP, benchmark (only on their flags)
diff --git a/graphify/skill-windows.md b/graphify/skill-windows.md
index b09ecca3c4..8f907cf0f1 100644
--- a/graphify/skill-windows.md
+++ b/graphify/skill-windows.md
@@ -124,7 +124,7 @@ if (-not $GRAPHIFY_PYTHON) {
 $Utf8NoBom = New-Object System.Text.UTF8Encoding $false
 [System.IO.File]::WriteAllText((Join-Path $PWD 'graphify-out\.graphify_python'), [string]$GRAPHIFY_PYTHON, $Utf8NoBom)
 # Save scan root so `graphify update` (no args) knows where to look next time
-[System.IO.File]::WriteAllText((Join-Path $PWD 'graphify-out\.graphify_root'), (Resolve-Path INPUT_PATH).Path, $Utf8NoBom)
+[System.IO.File]::WriteAllText((Join-Path $PWD 'graphify-out\.graphify_root'), (Resolve-Path "INPUT_PATH").Path, $Utf8NoBom)
 ```
 
 If the import succeeds, print nothing and move straight to Step 2.
@@ -203,7 +203,6 @@ For any code files detected, run AST extraction in parallel with Part B subagent
 import sys, json
 from graphify.extract import collect_files, extract
 from pathlib import Path
-import json
 
 code_files = []
 detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encoding="utf-8"))
@@ -572,7 +571,6 @@ Generate the HTML graph (always, unless `--no-viz`):
 
 ```powershell
 graphify export html  # auto-aggregates to community view if graph > 5000 nodes
-# or: graphify export html --no-viz
 ```
 
 ### Steps 6b-8 - Wiki, Neo4j, FalkorDB, SVG, GraphML, MCP, benchmark (only on their flags)
diff --git a/graphify/skill.md b/graphify/skill.md
index abd2811d23..65bb2ec32d 100644
--- a/graphify/skill.md
+++ b/graphify/skill.md
@@ -97,7 +97,7 @@ fi
 mkdir -p graphify-out
 "$PYTHON" -c "import sys; open('graphify-out/.graphify_python', 'w', encoding='utf-8').write(sys.executable)"
 # Save scan root so `graphify update` (no args) knows where to look next time
-echo "$(cd INPUT_PATH && pwd)" > graphify-out/.graphify_root
+echo "$(cd "INPUT_PATH" && pwd)" > graphify-out/.graphify_root
 ```
 
 If the import succeeds, print nothing and move straight to Step 2.
@@ -176,7 +176,6 @@ $(cat graphify-out/.graphify_python) -c "
 import sys, json
 from graphify.extract import collect_files, extract
 from pathlib import Path
-import json
 
 code_files = []
 detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encoding=\"utf-8\"))
@@ -545,7 +544,6 @@ Generate the HTML graph (always, unless `--no-viz`):
 
 ```bash
 graphify export html  # auto-aggregates to community view if graph > 5000 nodes
-# or: graphify export html --no-viz
 ```
 
 ### Steps 6b-8 - Wiki, Neo4j, FalkorDB, SVG, GraphML, MCP, benchmark (only on their flags)
diff --git a/graphify/skills/agents/references/add-watch.md b/graphify/skills/agents/references/add-watch.md
index 77844343e1..4504c838e6 100644
--- a/graphify/skills/agents/references/add-watch.md
+++ b/graphify/skills/agents/references/add-watch.md
@@ -24,7 +24,7 @@ except RuntimeError as e:
 "
 ```
 
-Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on `./raw` to merge the new file into the existing graph.
+Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on the scan root recorded in `graphify-out/.graphify_root` to merge the new file into the existing graph.
 
 Supported URL types (auto-detected):
 - YouTube / any video URL → audio downloaded via yt-dlp, transcribed to `.txt` on next run (requires `pip install 'graphifyy[video]'`)
diff --git a/graphify/skills/amp/references/add-watch.md b/graphify/skills/amp/references/add-watch.md
index 77844343e1..4504c838e6 100644
--- a/graphify/skills/amp/references/add-watch.md
+++ b/graphify/skills/amp/references/add-watch.md
@@ -24,7 +24,7 @@ except RuntimeError as e:
 "
 ```
 
-Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on `./raw` to merge the new file into the existing graph.
+Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on the scan root recorded in `graphify-out/.graphify_root` to merge the new file into the existing graph.
 
 Supported URL types (auto-detected):
 - YouTube / any video URL → audio downloaded via yt-dlp, transcribed to `.txt` on next run (requires `pip install 'graphifyy[video]'`)
diff --git a/graphify/skills/claude/references/add-watch.md b/graphify/skills/claude/references/add-watch.md
index 77844343e1..4504c838e6 100644
--- a/graphify/skills/claude/references/add-watch.md
+++ b/graphify/skills/claude/references/add-watch.md
@@ -24,7 +24,7 @@ except RuntimeError as e:
 "
 ```
 
-Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on `./raw` to merge the new file into the existing graph.
+Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on the scan root recorded in `graphify-out/.graphify_root` to merge the new file into the existing graph.
 
 Supported URL types (auto-detected):
 - YouTube / any video URL → audio downloaded via yt-dlp, transcribed to `.txt` on next run (requires `pip install 'graphifyy[video]'`)
diff --git a/graphify/skills/claw/references/add-watch.md b/graphify/skills/claw/references/add-watch.md
index 77844343e1..4504c838e6 100644
--- a/graphify/skills/claw/references/add-watch.md
+++ b/graphify/skills/claw/references/add-watch.md
@@ -24,7 +24,7 @@ except RuntimeError as e:
 "
 ```
 
-Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on `./raw` to merge the new file into the existing graph.
+Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on the scan root recorded in `graphify-out/.graphify_root` to merge the new file into the existing graph.
 
 Supported URL types (auto-detected):
 - YouTube / any video URL → audio downloaded via yt-dlp, transcribed to `.txt` on next run (requires `pip install 'graphifyy[video]'`)
diff --git a/graphify/skills/codex/references/add-watch.md b/graphify/skills/codex/references/add-watch.md
index 77844343e1..4504c838e6 100644
--- a/graphify/skills/codex/references/add-watch.md
+++ b/graphify/skills/codex/references/add-watch.md
@@ -24,7 +24,7 @@ except RuntimeError as e:
 "
 ```
 
-Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on `./raw` to merge the new file into the existing graph.
+Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on the scan root recorded in `graphify-out/.graphify_root` to merge the new file into the existing graph.
 
 Supported URL types (auto-detected):
 - YouTube / any video URL → audio downloaded via yt-dlp, transcribed to `.txt` on next run (requires `pip install 'graphifyy[video]'`)
diff --git a/graphify/skills/copilot/references/add-watch.md b/graphify/skills/copilot/references/add-watch.md
index 77844343e1..4504c838e6 100644
--- a/graphify/skills/copilot/references/add-watch.md
+++ b/graphify/skills/copilot/references/add-watch.md
@@ -24,7 +24,7 @@ except RuntimeError as e:
 "
 ```
 
-Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on `./raw` to merge the new file into the existing graph.
+Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on the scan root recorded in `graphify-out/.graphify_root` to merge the new file into the existing graph.
 
 Supported URL types (auto-detected):
 - YouTube / any video URL → audio downloaded via yt-dlp, transcribed to `.txt` on next run (requires `pip install 'graphifyy[video]'`)
diff --git a/graphify/skills/droid/references/add-watch.md b/graphify/skills/droid/references/add-watch.md
index 77844343e1..4504c838e6 100644
--- a/graphify/skills/droid/references/add-watch.md
+++ b/graphify/skills/droid/references/add-watch.md
@@ -24,7 +24,7 @@ except RuntimeError as e:
 "
 ```
 
-Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on `./raw` to merge the new file into the existing graph.
+Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on the scan root recorded in `graphify-out/.graphify_root` to merge the new file into the existing graph.
 
 Supported URL types (auto-detected):
 - YouTube / any video URL → audio downloaded via yt-dlp, transcribed to `.txt` on next run (requires `pip install 'graphifyy[video]'`)
diff --git a/graphify/skills/kilo/references/add-watch.md b/graphify/skills/kilo/references/add-watch.md
index 77844343e1..4504c838e6 100644
--- a/graphify/skills/kilo/references/add-watch.md
+++ b/graphify/skills/kilo/references/add-watch.md
@@ -24,7 +24,7 @@ except RuntimeError as e:
 "
 ```
 
-Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on `./raw` to merge the new file into the existing graph.
+Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on the scan root recorded in `graphify-out/.graphify_root` to merge the new file into the existing graph.
 
 Supported URL types (auto-detected):
 - YouTube / any video URL → audio downloaded via yt-dlp, transcribed to `.txt` on next run (requires `pip install 'graphifyy[video]'`)
diff --git a/graphify/skills/kiro/references/add-watch.md b/graphify/skills/kiro/references/add-watch.md
index 77844343e1..4504c838e6 100644
--- a/graphify/skills/kiro/references/add-watch.md
+++ b/graphify/skills/kiro/references/add-watch.md
@@ -24,7 +24,7 @@ except RuntimeError as e:
 "
 ```
 
-Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on `./raw` to merge the new file into the existing graph.
+Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on the scan root recorded in `graphify-out/.graphify_root` to merge the new file into the existing graph.
 
 Supported URL types (auto-detected):
 - YouTube / any video URL → audio downloaded via yt-dlp, transcribed to `.txt` on next run (requires `pip install 'graphifyy[video]'`)
diff --git a/graphify/skills/opencode/references/add-watch.md b/graphify/skills/opencode/references/add-watch.md
index 77844343e1..4504c838e6 100644
--- a/graphify/skills/opencode/references/add-watch.md
+++ b/graphify/skills/opencode/references/add-watch.md
@@ -24,7 +24,7 @@ except RuntimeError as e:
 "
 ```
 
-Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on `./raw` to merge the new file into the existing graph.
+Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on the scan root recorded in `graphify-out/.graphify_root` to merge the new file into the existing graph.
 
 Supported URL types (auto-detected):
 - YouTube / any video URL → audio downloaded via yt-dlp, transcribed to `.txt` on next run (requires `pip install 'graphifyy[video]'`)
diff --git a/graphify/skills/pi/references/add-watch.md b/graphify/skills/pi/references/add-watch.md
index 77844343e1..4504c838e6 100644
--- a/graphify/skills/pi/references/add-watch.md
+++ b/graphify/skills/pi/references/add-watch.md
@@ -24,7 +24,7 @@ except RuntimeError as e:
 "
 ```
 
-Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on `./raw` to merge the new file into the existing graph.
+Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on the scan root recorded in `graphify-out/.graphify_root` to merge the new file into the existing graph.
 
 Supported URL types (auto-detected):
 - YouTube / any video URL → audio downloaded via yt-dlp, transcribed to `.txt` on next run (requires `pip install 'graphifyy[video]'`)
diff --git a/graphify/skills/trae/references/add-watch.md b/graphify/skills/trae/references/add-watch.md
index 77844343e1..4504c838e6 100644
--- a/graphify/skills/trae/references/add-watch.md
+++ b/graphify/skills/trae/references/add-watch.md
@@ -24,7 +24,7 @@ except RuntimeError as e:
 "
 ```
 
-Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on `./raw` to merge the new file into the existing graph.
+Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on the scan root recorded in `graphify-out/.graphify_root` to merge the new file into the existing graph.
 
 Supported URL types (auto-detected):
 - YouTube / any video URL → audio downloaded via yt-dlp, transcribed to `.txt` on next run (requires `pip install 'graphifyy[video]'`)
diff --git a/graphify/skills/vscode/references/add-watch.md b/graphify/skills/vscode/references/add-watch.md
index 77844343e1..4504c838e6 100644
--- a/graphify/skills/vscode/references/add-watch.md
+++ b/graphify/skills/vscode/references/add-watch.md
@@ -24,7 +24,7 @@ except RuntimeError as e:
 "
 ```
 
-Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on `./raw` to merge the new file into the existing graph.
+Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on the scan root recorded in `graphify-out/.graphify_root` to merge the new file into the existing graph.
 
 Supported URL types (auto-detected):
 - YouTube / any video URL → audio downloaded via yt-dlp, transcribed to `.txt` on next run (requires `pip install 'graphifyy[video]'`)
diff --git a/graphify/skills/windows/references/add-watch.md b/graphify/skills/windows/references/add-watch.md
index 77844343e1..4504c838e6 100644
--- a/graphify/skills/windows/references/add-watch.md
+++ b/graphify/skills/windows/references/add-watch.md
@@ -24,7 +24,7 @@ except RuntimeError as e:
 "
 ```
 
-Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on `./raw` to merge the new file into the existing graph.
+Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on the scan root recorded in `graphify-out/.graphify_root` to merge the new file into the existing graph.
 
 Supported URL types (auto-detected):
 - YouTube / any video URL → audio downloaded via yt-dlp, transcribed to `.txt` on next run (requires `pip install 'graphifyy[video]'`)
diff --git a/tests/test_skillgen.py b/tests/test_skillgen.py
index 63a6f7c173..37d83962a9 100644
--- a/tests/test_skillgen.py
+++ b/tests/test_skillgen.py
@@ -58,6 +58,46 @@ def test_render_output_is_lf_only():
         assert not art.content.endswith("\n\n"), art.path
 
 
+def test_rendered_instructions_preserve_scan_root_and_runnable_commands():
+    """Generated agent instructions must remain safe for real roots and flags."""
+    platforms = gen.load_platforms()
+    artifacts = gen.render_all(platforms)
+    posix_cores = [
+        artifact
+        for artifact in artifacts
+        if 'echo "$(cd' in artifact.content
+    ]
+    assert posix_cores
+    for artifact in posix_cores:
+        assert 'cd "INPUT_PATH"' in artifact.content, artifact.path
+        assert (
+            "import sys, json\n"
+            "from graphify.extract import collect_files, extract\n"
+            "from pathlib import Path\n"
+            "import json\n"
+        ) not in artifact.content, artifact.path
+        assert "graphify export html --no-viz" not in artifact.content, artifact.path
+
+    windows_core = next(
+        artifact
+        for artifact in artifacts
+        if artifact.path == "graphify/skill-windows.md"
+    )
+    assert '(Resolve-Path "INPUT_PATH").Path' in windows_core.content
+
+    add_watch = [
+        artifact
+        for artifact in artifacts
+        if artifact.path.endswith("/references/add-watch.md")
+    ]
+    assert add_watch
+    for artifact in add_watch:
+        assert (
+            "run the `--update` pipeline on the scan root recorded in "
+            "`graphify-out/.graphify_root`"
+        ) in artifact.content, artifact.path
+
+
 def test_no_version_or_timestamp_in_output():
     """No generated artifact carries the package version string."""
     from graphify.__main__ import __version__
diff --git a/tools/skillgen/expected/graphify__skill-agents.md b/tools/skillgen/expected/graphify__skill-agents.md
index 190827d9ac..c14e438a30 100644
--- a/tools/skillgen/expected/graphify__skill-agents.md
+++ b/tools/skillgen/expected/graphify__skill-agents.md
@@ -97,7 +97,7 @@ fi
 mkdir -p graphify-out
 "$PYTHON" -c "import sys; open('graphify-out/.graphify_python', 'w', encoding='utf-8').write(sys.executable)"
 # Save scan root so `graphify update` (no args) knows where to look next time
-echo "$(cd INPUT_PATH && pwd)" > graphify-out/.graphify_root
+echo "$(cd "INPUT_PATH" && pwd)" > graphify-out/.graphify_root
 ```
 
 If the import succeeds, print nothing and move straight to Step 2.
@@ -176,7 +176,6 @@ $(cat graphify-out/.graphify_python) -c "
 import sys, json
 from graphify.extract import collect_files, extract
 from pathlib import Path
-import json
 
 code_files = []
 detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encoding=\"utf-8\"))
@@ -542,7 +541,6 @@ Generate the HTML graph (always, unless `--no-viz`):
 
 ```bash
 graphify export html  # auto-aggregates to community view if graph > 5000 nodes
-# or: graphify export html --no-viz
 ```
 
 ### Steps 6b-8 - Wiki, Neo4j, FalkorDB, SVG, GraphML, MCP, benchmark (only on their flags)
diff --git a/tools/skillgen/expected/graphify__skill-amp.md b/tools/skillgen/expected/graphify__skill-amp.md
index 190827d9ac..c14e438a30 100644
--- a/tools/skillgen/expected/graphify__skill-amp.md
+++ b/tools/skillgen/expected/graphify__skill-amp.md
@@ -97,7 +97,7 @@ fi
 mkdir -p graphify-out
 "$PYTHON" -c "import sys; open('graphify-out/.graphify_python', 'w', encoding='utf-8').write(sys.executable)"
 # Save scan root so `graphify update` (no args) knows where to look next time
-echo "$(cd INPUT_PATH && pwd)" > graphify-out/.graphify_root
+echo "$(cd "INPUT_PATH" && pwd)" > graphify-out/.graphify_root
 ```
 
 If the import succeeds, print nothing and move straight to Step 2.
@@ -176,7 +176,6 @@ $(cat graphify-out/.graphify_python) -c "
 import sys, json
 from graphify.extract import collect_files, extract
 from pathlib import Path
-import json
 
 code_files = []
 detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encoding=\"utf-8\"))
@@ -542,7 +541,6 @@ Generate the HTML graph (always, unless `--no-viz`):
 
 ```bash
 graphify export html  # auto-aggregates to community view if graph > 5000 nodes
-# or: graphify export html --no-viz
 ```
 
 ### Steps 6b-8 - Wiki, Neo4j, FalkorDB, SVG, GraphML, MCP, benchmark (only on their flags)
diff --git a/tools/skillgen/expected/graphify__skill-claw.md b/tools/skillgen/expected/graphify__skill-claw.md
index abd2811d23..65bb2ec32d 100644
--- a/tools/skillgen/expected/graphify__skill-claw.md
+++ b/tools/skillgen/expected/graphify__skill-claw.md
@@ -97,7 +97,7 @@ fi
 mkdir -p graphify-out
 "$PYTHON" -c "import sys; open('graphify-out/.graphify_python', 'w', encoding='utf-8').write(sys.executable)"
 # Save scan root so `graphify update` (no args) knows where to look next time
-echo "$(cd INPUT_PATH && pwd)" > graphify-out/.graphify_root
+echo "$(cd "INPUT_PATH" && pwd)" > graphify-out/.graphify_root
 ```
 
 If the import succeeds, print nothing and move straight to Step 2.
@@ -176,7 +176,6 @@ $(cat graphify-out/.graphify_python) -c "
 import sys, json
 from graphify.extract import collect_files, extract
 from pathlib import Path
-import json
 
 code_files = []
 detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encoding=\"utf-8\"))
@@ -545,7 +544,6 @@ Generate the HTML graph (always, unless `--no-viz`):
 
 ```bash
 graphify export html  # auto-aggregates to community view if graph > 5000 nodes
-# or: graphify export html --no-viz
 ```
 
 ### Steps 6b-8 - Wiki, Neo4j, FalkorDB, SVG, GraphML, MCP, benchmark (only on their flags)
diff --git a/tools/skillgen/expected/graphify__skill-codex.md b/tools/skillgen/expected/graphify__skill-codex.md
index af3f723c78..2bf76c2d76 100644
--- a/tools/skillgen/expected/graphify__skill-codex.md
+++ b/tools/skillgen/expected/graphify__skill-codex.md
@@ -97,7 +97,7 @@ fi
 mkdir -p graphify-out
 "$PYTHON" -c "import sys; open('graphify-out/.graphify_python', 'w', encoding='utf-8').write(sys.executable)"
 # Save scan root so `graphify update` (no args) knows where to look next time
-echo "$(cd INPUT_PATH && pwd)" > graphify-out/.graphify_root
+echo "$(cd "INPUT_PATH" && pwd)" > graphify-out/.graphify_root
 ```
 
 If the import succeeds, print nothing and move straight to Step 2.
@@ -176,7 +176,6 @@ $(cat graphify-out/.graphify_python) -c "
 import sys, json
 from graphify.extract import collect_files, extract
 from pathlib import Path
-import json
 
 code_files = []
 detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encoding=\"utf-8\"))
@@ -542,7 +541,6 @@ Generate the HTML graph (always, unless `--no-viz`):
 
 ```bash
 graphify export html  # auto-aggregates to community view if graph > 5000 nodes
-# or: graphify export html --no-viz
 ```
 
 ### Steps 6b-8 - Wiki, Neo4j, FalkorDB, SVG, GraphML, MCP, benchmark (only on their flags)
diff --git a/tools/skillgen/expected/graphify__skill-copilot.md b/tools/skillgen/expected/graphify__skill-copilot.md
index abd2811d23..65bb2ec32d 100644
--- a/tools/skillgen/expected/graphify__skill-copilot.md
+++ b/tools/skillgen/expected/graphify__skill-copilot.md
@@ -97,7 +97,7 @@ fi
 mkdir -p graphify-out
 "$PYTHON" -c "import sys; open('graphify-out/.graphify_python', 'w', encoding='utf-8').write(sys.executable)"
 # Save scan root so `graphify update` (no args) knows where to look next time
-echo "$(cd INPUT_PATH && pwd)" > graphify-out/.graphify_root
+echo "$(cd "INPUT_PATH" && pwd)" > graphify-out/.graphify_root
 ```
 
 If the import succeeds, print nothing and move straight to Step 2.
@@ -176,7 +176,6 @@ $(cat graphify-out/.graphify_python) -c "
 import sys, json
 from graphify.extract import collect_files, extract
 from pathlib import Path
-import json
 
 code_files = []
 detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encoding=\"utf-8\"))
@@ -545,7 +544,6 @@ Generate the HTML graph (always, unless `--no-viz`):
 
 ```bash
 graphify export html  # auto-aggregates to community view if graph > 5000 nodes
-# or: graphify export html --no-viz
 ```
 
 ### Steps 6b-8 - Wiki, Neo4j, FalkorDB, SVG, GraphML, MCP, benchmark (only on their flags)
diff --git a/tools/skillgen/expected/graphify__skill-droid.md b/tools/skillgen/expected/graphify__skill-droid.md
index fd148d485d..0353795e9e 100644
--- a/tools/skillgen/expected/graphify__skill-droid.md
+++ b/tools/skillgen/expected/graphify__skill-droid.md
@@ -97,7 +97,7 @@ fi
 mkdir -p graphify-out
 "$PYTHON" -c "import sys; open('graphify-out/.graphify_python', 'w', encoding='utf-8').write(sys.executable)"
 # Save scan root so `graphify update` (no args) knows where to look next time
-echo "$(cd INPUT_PATH && pwd)" > graphify-out/.graphify_root
+echo "$(cd "INPUT_PATH" && pwd)" > graphify-out/.graphify_root
 ```
 
 If the import succeeds, print nothing and move straight to Step 2.
@@ -176,7 +176,6 @@ $(cat graphify-out/.graphify_python) -c "
 import sys, json
 from graphify.extract import collect_files, extract
 from pathlib import Path
-import json
 
 code_files = []
 detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encoding=\"utf-8\"))
@@ -542,7 +541,6 @@ Generate the HTML graph (always, unless `--no-viz`):
 
 ```bash
 graphify export html  # auto-aggregates to community view if graph > 5000 nodes
-# or: graphify export html --no-viz
 ```
 
 ### Steps 6b-8 - Wiki, Neo4j, FalkorDB, SVG, GraphML, MCP, benchmark (only on their flags)
diff --git a/tools/skillgen/expected/graphify__skill-kilo.md b/tools/skillgen/expected/graphify__skill-kilo.md
index 3e70b050a4..0e38970de0 100644
--- a/tools/skillgen/expected/graphify__skill-kilo.md
+++ b/tools/skillgen/expected/graphify__skill-kilo.md
@@ -97,7 +97,7 @@ fi
 mkdir -p graphify-out
 "$PYTHON" -c "import sys; open('graphify-out/.graphify_python', 'w', encoding='utf-8').write(sys.executable)"
 # Save scan root so `graphify update` (no args) knows where to look next time
-echo "$(cd INPUT_PATH && pwd)" > graphify-out/.graphify_root
+echo "$(cd "INPUT_PATH" && pwd)" > graphify-out/.graphify_root
 ```
 
 If the import succeeds, print nothing and move straight to Step 2.
@@ -176,7 +176,6 @@ $(cat graphify-out/.graphify_python) -c "
 import sys, json
 from graphify.extract import collect_files, extract
 from pathlib import Path
-import json
 
 code_files = []
 detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encoding=\"utf-8\"))
@@ -545,7 +544,6 @@ Generate the HTML graph (always, unless `--no-viz`):
 
 ```bash
 graphify export html  # auto-aggregates to community view if graph > 5000 nodes
-# or: graphify export html --no-viz
 ```
 
 ### Steps 6b-8 - Wiki, Neo4j, FalkorDB, SVG, GraphML, MCP, benchmark (only on their flags)
diff --git a/tools/skillgen/expected/graphify__skill-kiro.md b/tools/skillgen/expected/graphify__skill-kiro.md
index abd2811d23..65bb2ec32d 100644
--- a/tools/skillgen/expected/graphify__skill-kiro.md
+++ b/tools/skillgen/expected/graphify__skill-kiro.md
@@ -97,7 +97,7 @@ fi
 mkdir -p graphify-out
 "$PYTHON" -c "import sys; open('graphify-out/.graphify_python', 'w', encoding='utf-8').write(sys.executable)"
 # Save scan root so `graphify update` (no args) knows where to look next time
-echo "$(cd INPUT_PATH && pwd)" > graphify-out/.graphify_root
+echo "$(cd "INPUT_PATH" && pwd)" > graphify-out/.graphify_root
 ```
 
 If the import succeeds, print nothing and move straight to Step 2.
@@ -176,7 +176,6 @@ $(cat graphify-out/.graphify_python) -c "
 import sys, json
 from graphify.extract import collect_files, extract
 from pathlib import Path
-import json
 
 code_files = []
 detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encoding=\"utf-8\"))
@@ -545,7 +544,6 @@ Generate the HTML graph (always, unless `--no-viz`):
 
 ```bash
 graphify export html  # auto-aggregates to community view if graph > 5000 nodes
-# or: graphify export html --no-viz
 ```
 
 ### Steps 6b-8 - Wiki, Neo4j, FalkorDB, SVG, GraphML, MCP, benchmark (only on their flags)
diff --git a/tools/skillgen/expected/graphify__skill-opencode.md b/tools/skillgen/expected/graphify__skill-opencode.md
index 91ced60675..0022c7a243 100644
--- a/tools/skillgen/expected/graphify__skill-opencode.md
+++ b/tools/skillgen/expected/graphify__skill-opencode.md
@@ -97,7 +97,7 @@ fi
 mkdir -p graphify-out
 "$PYTHON" -c "import sys; open('graphify-out/.graphify_python', 'w', encoding='utf-8').write(sys.executable)"
 # Save scan root so `graphify update` (no args) knows where to look next time
-echo "$(cd INPUT_PATH && pwd)" > graphify-out/.graphify_root
+echo "$(cd "INPUT_PATH" && pwd)" > graphify-out/.graphify_root
 ```
 
 If the import succeeds, print nothing and move straight to Step 2.
@@ -176,7 +176,6 @@ $(cat graphify-out/.graphify_python) -c "
 import sys, json
 from graphify.extract import collect_files, extract
 from pathlib import Path
-import json
 
 code_files = []
 detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encoding=\"utf-8\"))
@@ -537,7 +536,6 @@ Generate the HTML graph (always, unless `--no-viz`):
 
 ```bash
 graphify export html  # auto-aggregates to community view if graph > 5000 nodes
-# or: graphify export html --no-viz
 ```
 
 ### Steps 6b-8 - Wiki, Neo4j, FalkorDB, SVG, GraphML, MCP, benchmark (only on their flags)
diff --git a/tools/skillgen/expected/graphify__skill-pi.md b/tools/skillgen/expected/graphify__skill-pi.md
index abd2811d23..65bb2ec32d 100644
--- a/tools/skillgen/expected/graphify__skill-pi.md
+++ b/tools/skillgen/expected/graphify__skill-pi.md
@@ -97,7 +97,7 @@ fi
 mkdir -p graphify-out
 "$PYTHON" -c "import sys; open('graphify-out/.graphify_python', 'w', encoding='utf-8').write(sys.executable)"
 # Save scan root so `graphify update` (no args) knows where to look next time
-echo "$(cd INPUT_PATH && pwd)" > graphify-out/.graphify_root
+echo "$(cd "INPUT_PATH" && pwd)" > graphify-out/.graphify_root
 ```
 
 If the import succeeds, print nothing and move straight to Step 2.
@@ -176,7 +176,6 @@ $(cat graphify-out/.graphify_python) -c "
 import sys, json
 from graphify.extract import collect_files, extract
 from pathlib import Path
-import json
 
 code_files = []
 detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encoding=\"utf-8\"))
@@ -545,7 +544,6 @@ Generate the HTML graph (always, unless `--no-viz`):
 
 ```bash
 graphify export html  # auto-aggregates to community view if graph > 5000 nodes
-# or: graphify export html --no-viz
 ```
 
 ### Steps 6b-8 - Wiki, Neo4j, FalkorDB, SVG, GraphML, MCP, benchmark (only on their flags)
diff --git a/tools/skillgen/expected/graphify__skill-trae.md b/tools/skillgen/expected/graphify__skill-trae.md
index 050667bc20..9fb9a113fb 100644
--- a/tools/skillgen/expected/graphify__skill-trae.md
+++ b/tools/skillgen/expected/graphify__skill-trae.md
@@ -97,7 +97,7 @@ fi
 mkdir -p graphify-out
 "$PYTHON" -c "import sys; open('graphify-out/.graphify_python', 'w', encoding='utf-8').write(sys.executable)"
 # Save scan root so `graphify update` (no args) knows where to look next time
-echo "$(cd INPUT_PATH && pwd)" > graphify-out/.graphify_root
+echo "$(cd "INPUT_PATH" && pwd)" > graphify-out/.graphify_root
 ```
 
 If the import succeeds, print nothing and move straight to Step 2.
@@ -176,7 +176,6 @@ $(cat graphify-out/.graphify_python) -c "
 import sys, json
 from graphify.extract import collect_files, extract
 from pathlib import Path
-import json
 
 code_files = []
 detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encoding=\"utf-8\"))
@@ -543,7 +542,6 @@ Generate the HTML graph (always, unless `--no-viz`):
 
 ```bash
 graphify export html  # auto-aggregates to community view if graph > 5000 nodes
-# or: graphify export html --no-viz
 ```
 
 ### Steps 6b-8 - Wiki, Neo4j, FalkorDB, SVG, GraphML, MCP, benchmark (only on their flags)
diff --git a/tools/skillgen/expected/graphify__skill-vscode.md b/tools/skillgen/expected/graphify__skill-vscode.md
index 20c7c0835c..310911e713 100644
--- a/tools/skillgen/expected/graphify__skill-vscode.md
+++ b/tools/skillgen/expected/graphify__skill-vscode.md
@@ -97,7 +97,7 @@ fi
 mkdir -p graphify-out
 "$PYTHON" -c "import sys; open('graphify-out/.graphify_python', 'w', encoding='utf-8').write(sys.executable)"
 # Save scan root so `graphify update` (no args) knows where to look next time
-echo "$(cd INPUT_PATH && pwd)" > graphify-out/.graphify_root
+echo "$(cd "INPUT_PATH" && pwd)" > graphify-out/.graphify_root
 ```
 
 If the import succeeds, print nothing and move straight to Step 2.
@@ -176,7 +176,6 @@ $(cat graphify-out/.graphify_python) -c "
 import sys, json
 from graphify.extract import collect_files, extract
 from pathlib import Path
-import json
 
 code_files = []
 detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encoding=\"utf-8\"))
@@ -541,7 +540,6 @@ Generate the HTML graph (always, unless `--no-viz`):
 
 ```bash
 graphify export html  # auto-aggregates to community view if graph > 5000 nodes
-# or: graphify export html --no-viz
 ```
 
 ### Steps 6b-8 - Wiki, Neo4j, FalkorDB, SVG, GraphML, MCP, benchmark (only on their flags)
diff --git a/tools/skillgen/expected/graphify__skill-windows.md b/tools/skillgen/expected/graphify__skill-windows.md
index b09ecca3c4..8f907cf0f1 100644
--- a/tools/skillgen/expected/graphify__skill-windows.md
+++ b/tools/skillgen/expected/graphify__skill-windows.md
@@ -124,7 +124,7 @@ if (-not $GRAPHIFY_PYTHON) {
 $Utf8NoBom = New-Object System.Text.UTF8Encoding $false
 [System.IO.File]::WriteAllText((Join-Path $PWD 'graphify-out\.graphify_python'), [string]$GRAPHIFY_PYTHON, $Utf8NoBom)
 # Save scan root so `graphify update` (no args) knows where to look next time
-[System.IO.File]::WriteAllText((Join-Path $PWD 'graphify-out\.graphify_root'), (Resolve-Path INPUT_PATH).Path, $Utf8NoBom)
+[System.IO.File]::WriteAllText((Join-Path $PWD 'graphify-out\.graphify_root'), (Resolve-Path "INPUT_PATH").Path, $Utf8NoBom)
 ```
 
 If the import succeeds, print nothing and move straight to Step 2.
@@ -203,7 +203,6 @@ For any code files detected, run AST extraction in parallel with Part B subagent
 import sys, json
 from graphify.extract import collect_files, extract
 from pathlib import Path
-import json
 
 code_files = []
 detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encoding="utf-8"))
@@ -572,7 +571,6 @@ Generate the HTML graph (always, unless `--no-viz`):
 
 ```powershell
 graphify export html  # auto-aggregates to community view if graph > 5000 nodes
-# or: graphify export html --no-viz
 ```
 
 ### Steps 6b-8 - Wiki, Neo4j, FalkorDB, SVG, GraphML, MCP, benchmark (only on their flags)
diff --git a/tools/skillgen/expected/graphify__skill.md b/tools/skillgen/expected/graphify__skill.md
index abd2811d23..65bb2ec32d 100644
--- a/tools/skillgen/expected/graphify__skill.md
+++ b/tools/skillgen/expected/graphify__skill.md
@@ -97,7 +97,7 @@ fi
 mkdir -p graphify-out
 "$PYTHON" -c "import sys; open('graphify-out/.graphify_python', 'w', encoding='utf-8').write(sys.executable)"
 # Save scan root so `graphify update` (no args) knows where to look next time
-echo "$(cd INPUT_PATH && pwd)" > graphify-out/.graphify_root
+echo "$(cd "INPUT_PATH" && pwd)" > graphify-out/.graphify_root
 ```
 
 If the import succeeds, print nothing and move straight to Step 2.
@@ -176,7 +176,6 @@ $(cat graphify-out/.graphify_python) -c "
 import sys, json
 from graphify.extract import collect_files, extract
 from pathlib import Path
-import json
 
 code_files = []
 detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encoding=\"utf-8\"))
@@ -545,7 +544,6 @@ Generate the HTML graph (always, unless `--no-viz`):
 
 ```bash
 graphify export html  # auto-aggregates to community view if graph > 5000 nodes
-# or: graphify export html --no-viz
 ```
 
 ### Steps 6b-8 - Wiki, Neo4j, FalkorDB, SVG, GraphML, MCP, benchmark (only on their flags)
diff --git a/tools/skillgen/expected/graphify__skills__agents__references__add-watch.md b/tools/skillgen/expected/graphify__skills__agents__references__add-watch.md
index 77844343e1..4504c838e6 100644
--- a/tools/skillgen/expected/graphify__skills__agents__references__add-watch.md
+++ b/tools/skillgen/expected/graphify__skills__agents__references__add-watch.md
@@ -24,7 +24,7 @@ except RuntimeError as e:
 "
 ```
 
-Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on `./raw` to merge the new file into the existing graph.
+Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on the scan root recorded in `graphify-out/.graphify_root` to merge the new file into the existing graph.
 
 Supported URL types (auto-detected):
 - YouTube / any video URL → audio downloaded via yt-dlp, transcribed to `.txt` on next run (requires `pip install 'graphifyy[video]'`)
diff --git a/tools/skillgen/expected/graphify__skills__amp__references__add-watch.md b/tools/skillgen/expected/graphify__skills__amp__references__add-watch.md
index 77844343e1..4504c838e6 100644
--- a/tools/skillgen/expected/graphify__skills__amp__references__add-watch.md
+++ b/tools/skillgen/expected/graphify__skills__amp__references__add-watch.md
@@ -24,7 +24,7 @@ except RuntimeError as e:
 "
 ```
 
-Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on `./raw` to merge the new file into the existing graph.
+Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on the scan root recorded in `graphify-out/.graphify_root` to merge the new file into the existing graph.
 
 Supported URL types (auto-detected):
 - YouTube / any video URL → audio downloaded via yt-dlp, transcribed to `.txt` on next run (requires `pip install 'graphifyy[video]'`)
diff --git a/tools/skillgen/expected/graphify__skills__claude__references__add-watch.md b/tools/skillgen/expected/graphify__skills__claude__references__add-watch.md
index 77844343e1..4504c838e6 100644
--- a/tools/skillgen/expected/graphify__skills__claude__references__add-watch.md
+++ b/tools/skillgen/expected/graphify__skills__claude__references__add-watch.md
@@ -24,7 +24,7 @@ except RuntimeError as e:
 "
 ```
 
-Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on `./raw` to merge the new file into the existing graph.
+Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on the scan root recorded in `graphify-out/.graphify_root` to merge the new file into the existing graph.
 
 Supported URL types (auto-detected):
 - YouTube / any video URL → audio downloaded via yt-dlp, transcribed to `.txt` on next run (requires `pip install 'graphifyy[video]'`)
diff --git a/tools/skillgen/expected/graphify__skills__claw__references__add-watch.md b/tools/skillgen/expected/graphify__skills__claw__references__add-watch.md
index 77844343e1..4504c838e6 100644
--- a/tools/skillgen/expected/graphify__skills__claw__references__add-watch.md
+++ b/tools/skillgen/expected/graphify__skills__claw__references__add-watch.md
@@ -24,7 +24,7 @@ except RuntimeError as e:
 "
 ```
 
-Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on `./raw` to merge the new file into the existing graph.
+Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on the scan root recorded in `graphify-out/.graphify_root` to merge the new file into the existing graph.
 
 Supported URL types (auto-detected):
 - YouTube / any video URL → audio downloaded via yt-dlp, transcribed to `.txt` on next run (requires `pip install 'graphifyy[video]'`)
diff --git a/tools/skillgen/expected/graphify__skills__codex__references__add-watch.md b/tools/skillgen/expected/graphify__skills__codex__references__add-watch.md
index 77844343e1..4504c838e6 100644
--- a/tools/skillgen/expected/graphify__skills__codex__references__add-watch.md
+++ b/tools/skillgen/expected/graphify__skills__codex__references__add-watch.md
@@ -24,7 +24,7 @@ except RuntimeError as e:
 "
 ```
 
-Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on `./raw` to merge the new file into the existing graph.
+Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on the scan root recorded in `graphify-out/.graphify_root` to merge the new file into the existing graph.
 
 Supported URL types (auto-detected):
 - YouTube / any video URL → audio downloaded via yt-dlp, transcribed to `.txt` on next run (requires `pip install 'graphifyy[video]'`)
diff --git a/tools/skillgen/expected/graphify__skills__copilot__references__add-watch.md b/tools/skillgen/expected/graphify__skills__copilot__references__add-watch.md
index 77844343e1..4504c838e6 100644
--- a/tools/skillgen/expected/graphify__skills__copilot__references__add-watch.md
+++ b/tools/skillgen/expected/graphify__skills__copilot__references__add-watch.md
@@ -24,7 +24,7 @@ except RuntimeError as e:
 "
 ```
 
-Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on `./raw` to merge the new file into the existing graph.
+Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on the scan root recorded in `graphify-out/.graphify_root` to merge the new file into the existing graph.
 
 Supported URL types (auto-detected):
 - YouTube / any video URL → audio downloaded via yt-dlp, transcribed to `.txt` on next run (requires `pip install 'graphifyy[video]'`)
diff --git a/tools/skillgen/expected/graphify__skills__droid__references__add-watch.md b/tools/skillgen/expected/graphify__skills__droid__references__add-watch.md
index 77844343e1..4504c838e6 100644
--- a/tools/skillgen/expected/graphify__skills__droid__references__add-watch.md
+++ b/tools/skillgen/expected/graphify__skills__droid__references__add-watch.md
@@ -24,7 +24,7 @@ except RuntimeError as e:
 "
 ```
 
-Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on `./raw` to merge the new file into the existing graph.
+Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on the scan root recorded in `graphify-out/.graphify_root` to merge the new file into the existing graph.
 
 Supported URL types (auto-detected):
 - YouTube / any video URL → audio downloaded via yt-dlp, transcribed to `.txt` on next run (requires `pip install 'graphifyy[video]'`)
diff --git a/tools/skillgen/expected/graphify__skills__kilo__references__add-watch.md b/tools/skillgen/expected/graphify__skills__kilo__references__add-watch.md
index 77844343e1..4504c838e6 100644
--- a/tools/skillgen/expected/graphify__skills__kilo__references__add-watch.md
+++ b/tools/skillgen/expected/graphify__skills__kilo__references__add-watch.md
@@ -24,7 +24,7 @@ except RuntimeError as e:
 "
 ```
 
-Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on `./raw` to merge the new file into the existing graph.
+Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on the scan root recorded in `graphify-out/.graphify_root` to merge the new file into the existing graph.
 
 Supported URL types (auto-detected):
 - YouTube / any video URL → audio downloaded via yt-dlp, transcribed to `.txt` on next run (requires `pip install 'graphifyy[video]'`)
diff --git a/tools/skillgen/expected/graphify__skills__kiro__references__add-watch.md b/tools/skillgen/expected/graphify__skills__kiro__references__add-watch.md
index 77844343e1..4504c838e6 100644
--- a/tools/skillgen/expected/graphify__skills__kiro__references__add-watch.md
+++ b/tools/skillgen/expected/graphify__skills__kiro__references__add-watch.md
@@ -24,7 +24,7 @@ except RuntimeError as e:
 "
 ```
 
-Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on `./raw` to merge the new file into the existing graph.
+Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on the scan root recorded in `graphify-out/.graphify_root` to merge the new file into the existing graph.
 
 Supported URL types (auto-detected):
 - YouTube / any video URL → audio downloaded via yt-dlp, transcribed to `.txt` on next run (requires `pip install 'graphifyy[video]'`)
diff --git a/tools/skillgen/expected/graphify__skills__opencode__references__add-watch.md b/tools/skillgen/expected/graphify__skills__opencode__references__add-watch.md
index 77844343e1..4504c838e6 100644
--- a/tools/skillgen/expected/graphify__skills__opencode__references__add-watch.md
+++ b/tools/skillgen/expected/graphify__skills__opencode__references__add-watch.md
@@ -24,7 +24,7 @@ except RuntimeError as e:
 "
 ```
 
-Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on `./raw` to merge the new file into the existing graph.
+Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on the scan root recorded in `graphify-out/.graphify_root` to merge the new file into the existing graph.
 
 Supported URL types (auto-detected):
 - YouTube / any video URL → audio downloaded via yt-dlp, transcribed to `.txt` on next run (requires `pip install 'graphifyy[video]'`)
diff --git a/tools/skillgen/expected/graphify__skills__pi__references__add-watch.md b/tools/skillgen/expected/graphify__skills__pi__references__add-watch.md
index 77844343e1..4504c838e6 100644
--- a/tools/skillgen/expected/graphify__skills__pi__references__add-watch.md
+++ b/tools/skillgen/expected/graphify__skills__pi__references__add-watch.md
@@ -24,7 +24,7 @@ except RuntimeError as e:
 "
 ```
 
-Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on `./raw` to merge the new file into the existing graph.
+Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on the scan root recorded in `graphify-out/.graphify_root` to merge the new file into the existing graph.
 
 Supported URL types (auto-detected):
 - YouTube / any video URL → audio downloaded via yt-dlp, transcribed to `.txt` on next run (requires `pip install 'graphifyy[video]'`)
diff --git a/tools/skillgen/expected/graphify__skills__trae__references__add-watch.md b/tools/skillgen/expected/graphify__skills__trae__references__add-watch.md
index 77844343e1..4504c838e6 100644
--- a/tools/skillgen/expected/graphify__skills__trae__references__add-watch.md
+++ b/tools/skillgen/expected/graphify__skills__trae__references__add-watch.md
@@ -24,7 +24,7 @@ except RuntimeError as e:
 "
 ```
 
-Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on `./raw` to merge the new file into the existing graph.
+Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on the scan root recorded in `graphify-out/.graphify_root` to merge the new file into the existing graph.
 
 Supported URL types (auto-detected):
 - YouTube / any video URL → audio downloaded via yt-dlp, transcribed to `.txt` on next run (requires `pip install 'graphifyy[video]'`)
diff --git a/tools/skillgen/expected/graphify__skills__vscode__references__add-watch.md b/tools/skillgen/expected/graphify__skills__vscode__references__add-watch.md
index 77844343e1..4504c838e6 100644
--- a/tools/skillgen/expected/graphify__skills__vscode__references__add-watch.md
+++ b/tools/skillgen/expected/graphify__skills__vscode__references__add-watch.md
@@ -24,7 +24,7 @@ except RuntimeError as e:
 "
 ```
 
-Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on `./raw` to merge the new file into the existing graph.
+Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on the scan root recorded in `graphify-out/.graphify_root` to merge the new file into the existing graph.
 
 Supported URL types (auto-detected):
 - YouTube / any video URL → audio downloaded via yt-dlp, transcribed to `.txt` on next run (requires `pip install 'graphifyy[video]'`)
diff --git a/tools/skillgen/expected/graphify__skills__windows__references__add-watch.md b/tools/skillgen/expected/graphify__skills__windows__references__add-watch.md
index 77844343e1..4504c838e6 100644
--- a/tools/skillgen/expected/graphify__skills__windows__references__add-watch.md
+++ b/tools/skillgen/expected/graphify__skills__windows__references__add-watch.md
@@ -24,7 +24,7 @@ except RuntimeError as e:
 "
 ```
 
-Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on `./raw` to merge the new file into the existing graph.
+Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on the scan root recorded in `graphify-out/.graphify_root` to merge the new file into the existing graph.
 
 Supported URL types (auto-detected):
 - YouTube / any video URL → audio downloaded via yt-dlp, transcribed to `.txt` on next run (requires `pip install 'graphifyy[video]'`)
diff --git a/tools/skillgen/fragments/core/core.md b/tools/skillgen/fragments/core/core.md
index c527a12563..a16b7152fd 100644
--- a/tools/skillgen/fragments/core/core.md
+++ b/tools/skillgen/fragments/core/core.md
@@ -135,7 +135,6 @@ $(cat graphify-out/.graphify_python) -c "
 import sys, json
 from graphify.extract import collect_files, extract
 from pathlib import Path
-import json
 
 code_files = []
 detect = json.loads(Path('graphify-out/.graphify_detect.json').read_text(encoding=\"utf-8\"))
@@ -480,7 +479,6 @@ Generate the HTML graph (always, unless `--no-viz`):
 
 ```bash
 graphify export html  # auto-aggregates to community view if graph > 5000 nodes
-# or: graphify export html --no-viz
 ```
 
 ### Steps 6b-8 - Wiki, Neo4j, FalkorDB, SVG, GraphML, MCP, benchmark (only on their flags)
diff --git a/tools/skillgen/fragments/references/shared/add-watch.md b/tools/skillgen/fragments/references/shared/add-watch.md
index 77844343e1..4504c838e6 100644
--- a/tools/skillgen/fragments/references/shared/add-watch.md
+++ b/tools/skillgen/fragments/references/shared/add-watch.md
@@ -24,7 +24,7 @@ except RuntimeError as e:
 "
 ```
 
-Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on `./raw` to merge the new file into the existing graph.
+Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. If the command exits with an error, tell the user what went wrong - do not silently continue. After a successful save, automatically run the `--update` pipeline on the scan root recorded in `graphify-out/.graphify_root` to merge the new file into the existing graph.
 
 Supported URL types (auto-detected):
 - YouTube / any video URL → audio downloaded via yt-dlp, transcribed to `.txt` on next run (requires `pip install 'graphifyy[video]'`)
diff --git a/tools/skillgen/fragments/shell/posix.md b/tools/skillgen/fragments/shell/posix.md
index 3534417d23..54ae63f87c 100644
--- a/tools/skillgen/fragments/shell/posix.md
+++ b/tools/skillgen/fragments/shell/posix.md
@@ -31,7 +31,7 @@ fi
 mkdir -p graphify-out
 "$PYTHON" -c "import sys; open('graphify-out/.graphify_python', 'w', encoding='utf-8').write(sys.executable)"
 # Save scan root so `graphify update` (no args) knows where to look next time
-echo "$(cd INPUT_PATH && pwd)" > graphify-out/.graphify_root
+echo "$(cd "INPUT_PATH" && pwd)" > graphify-out/.graphify_root
 ```
 
 If the import succeeds, print nothing and move straight to Step 2.
diff --git a/tools/skillgen/fragments/shell/powershell.md b/tools/skillgen/fragments/shell/powershell.md
index 71e493cf8d..62caf5c9ec 100644
--- a/tools/skillgen/fragments/shell/powershell.md
+++ b/tools/skillgen/fragments/shell/powershell.md
@@ -58,7 +58,7 @@ if (-not $GRAPHIFY_PYTHON) {
 $Utf8NoBom = New-Object System.Text.UTF8Encoding $false
 [System.IO.File]::WriteAllText((Join-Path $PWD 'graphify-out\.graphify_python'), [string]$GRAPHIFY_PYTHON, $Utf8NoBom)
 # Save scan root so `graphify update` (no args) knows where to look next time
-[System.IO.File]::WriteAllText((Join-Path $PWD 'graphify-out\.graphify_root'), (Resolve-Path INPUT_PATH).Path, $Utf8NoBom)
+[System.IO.File]::WriteAllText((Join-Path $PWD 'graphify-out\.graphify_root'), (Resolve-Path "INPUT_PATH").Path, $Utf8NoBom)
 ```
 
 If the import succeeds, print nothing and move straight to Step 2.