fix: harden generated Graphify commands

graphify/skill-agents.md

@@ -534,14 +534,14 @@ If `--obsidian` was given:
 - If `--obsidian-dir <path>` was also given, pass it via `--dir`. Otherwise defaults to `graphify-out/obsidian`.
 
 ```bash
-graphify export obsidian
-# or with custom dir: graphify export obsidian --dir ~/vaults/my-project
+$(cat graphify-out/.graphify_python) -m graphify export obsidian
+# Add `--dir ~/vaults/my-project` to use a custom directory.
 ```
 
 Generate the HTML graph (always, unless `--no-viz`):
 
 ```bash
-graphify export html  # auto-aggregates to community view if graph > 5000 nodes
+$(cat graphify-out/.graphify_python) -m graphify export html  # auto-aggregates to community view if graph > 5000 nodes
 ```
 
 ### Steps 6b-8 - Wiki, Neo4j, FalkorDB, SVG, GraphML, MCP, benchmark (only on their flags)
@@ -681,7 +681,7 @@ Both are non-default subcommands. `--update` re-extracts only new or changed fil
 When `graphify-out/graph.json` already exists and the user asks a question about the corpus, answer from the graph rather than rebuilding it:
 
 ```bash
-graphify query "<question>"
+$(cat graphify-out/.graphify_python) -m graphify query "<question>"
 ```
 
 Before traversal, expand the question against the graph's own vocabulary so a wording mismatch does not collapse the answer to noise. If the `graphify query` CLI is unavailable, fall back to an inline NetworkX traversal of `graphify-out/graph.json`. Answer using only what the graph output contains, and quote `source_location` when citing a specific fact. For that vocab-expansion step, the BFS/DFS traversal modes, the `--budget` cap, the NetworkX fallback, `save-result` feedback, and the `/graphify path` and `/graphify explain` flows, see `references/query.md`.

graphify/skill-aider.md

@@ -1200,18 +1200,18 @@ from graphify.ingest import ingest
 from pathlib import Path
 
 try:
-    out = ingest('URL', Path('./raw'), author='AUTHOR', contributor='CONTRIBUTOR')
+    out = ingest(sys.argv[1], Path('./raw'), author=sys.argv[2] or None, contributor=sys.argv[3] or None)
     print(f'Saved to {out}')
 except ValueError as e:
     print(f'error: {e}', file=sys.stderr)
     sys.exit(1)
 except RuntimeError as e:
     print(f'error: {e}', file=sys.stderr)
     sys.exit(1)
-"
+" "URL" "AUTHOR" "CONTRIBUTOR"
 ```
 
-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 and pass the user's `AUTHOR` or `CONTRIBUTOR` when provided; use an empty string for either omitted value. 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.
 
 Supported URL types (auto-detected):
 - Twitter/X → fetched via oEmbed, saved as `.md` with tweet text and author

graphify/skill-amp.md

@@ -534,14 +534,14 @@ If `--obsidian` was given:
 - If `--obsidian-dir <path>` was also given, pass it via `--dir`. Otherwise defaults to `graphify-out/obsidian`.
 
 ```bash
-graphify export obsidian
-# or with custom dir: graphify export obsidian --dir ~/vaults/my-project
+$(cat graphify-out/.graphify_python) -m graphify export obsidian
+# Add `--dir ~/vaults/my-project` to use a custom directory.
 ```
 
 Generate the HTML graph (always, unless `--no-viz`):
 
 ```bash
-graphify export html  # auto-aggregates to community view if graph > 5000 nodes
+$(cat graphify-out/.graphify_python) -m graphify export html  # auto-aggregates to community view if graph > 5000 nodes
 ```
 
 ### Steps 6b-8 - Wiki, Neo4j, FalkorDB, SVG, GraphML, MCP, benchmark (only on their flags)
@@ -681,7 +681,7 @@ Both are non-default subcommands. `--update` re-extracts only new or changed fil
 When `graphify-out/graph.json` already exists and the user asks a question about the corpus, answer from the graph rather than rebuilding it:
 
 ```bash
-graphify query "<question>"
+$(cat graphify-out/.graphify_python) -m graphify query "<question>"
 ```
 
 Before traversal, expand the question against the graph's own vocabulary so a wording mismatch does not collapse the answer to noise. If the `graphify query` CLI is unavailable, fall back to an inline NetworkX traversal of `graphify-out/graph.json`. Answer using only what the graph output contains, and quote `source_location` when citing a specific fact. For that vocab-expansion step, the BFS/DFS traversal modes, the `--budget` cap, the NetworkX fallback, `save-result` feedback, and the `/graphify path` and `/graphify explain` flows, see `references/query.md`.

graphify/skill-claw.md

@@ -537,14 +537,14 @@ If `--obsidian` was given:
 - If `--obsidian-dir <path>` was also given, pass it via `--dir`. Otherwise defaults to `graphify-out/obsidian`.
 
 ```bash
-graphify export obsidian
-# or with custom dir: graphify export obsidian --dir ~/vaults/my-project
+$(cat graphify-out/.graphify_python) -m graphify export obsidian
+# Add `--dir ~/vaults/my-project` to use a custom directory.
 ```
 
 Generate the HTML graph (always, unless `--no-viz`):
 
 ```bash
-graphify export html  # auto-aggregates to community view if graph > 5000 nodes
+$(cat graphify-out/.graphify_python) -m graphify export html  # auto-aggregates to community view if graph > 5000 nodes
 ```
 
 ### Steps 6b-8 - Wiki, Neo4j, FalkorDB, SVG, GraphML, MCP, benchmark (only on their flags)
@@ -684,7 +684,7 @@ Both are non-default subcommands. `--update` re-extracts only new or changed fil
 When `graphify-out/graph.json` already exists and the user asks a question about the corpus, answer from the graph rather than rebuilding it:
 
 ```bash
-graphify query "<question>"
+$(cat graphify-out/.graphify_python) -m graphify query "<question>"
 ```
 
 Before traversal, expand the question against the graph's own vocabulary so a wording mismatch does not collapse the answer to noise. If the `graphify query` CLI is unavailable, fall back to an inline NetworkX traversal of `graphify-out/graph.json`. Answer using only what the graph output contains, and quote `source_location` when citing a specific fact. For that vocab-expansion step, the BFS/DFS traversal modes, the `--budget` cap, the NetworkX fallback, `save-result` feedback, and the `/graphify path` and `/graphify explain` flows, see `references/query.md`.

graphify/skill-codex.md

@@ -534,14 +534,14 @@ If `--obsidian` was given:
 - If `--obsidian-dir <path>` was also given, pass it via `--dir`. Otherwise defaults to `graphify-out/obsidian`.
 
 ```bash
-graphify export obsidian
-# or with custom dir: graphify export obsidian --dir ~/vaults/my-project
+$(cat graphify-out/.graphify_python) -m graphify export obsidian
+# Add `--dir ~/vaults/my-project` to use a custom directory.
 ```
 
 Generate the HTML graph (always, unless `--no-viz`):
 
 ```bash
-graphify export html  # auto-aggregates to community view if graph > 5000 nodes
+$(cat graphify-out/.graphify_python) -m graphify export html  # auto-aggregates to community view if graph > 5000 nodes
 ```
 
 ### Steps 6b-8 - Wiki, Neo4j, FalkorDB, SVG, GraphML, MCP, benchmark (only on their flags)
@@ -681,7 +681,7 @@ Both are non-default subcommands. `--update` re-extracts only new or changed fil
 When `graphify-out/graph.json` already exists and the user asks a question about the corpus, answer from the graph rather than rebuilding it:
 
 ```bash
-graphify query "<question>"
+$(cat graphify-out/.graphify_python) -m graphify query "<question>"
 ```
 
 Before traversal, expand the question against the graph's own vocabulary so a wording mismatch does not collapse the answer to noise. If the `graphify query` CLI is unavailable, fall back to an inline NetworkX traversal of `graphify-out/graph.json`. Answer using only what the graph output contains, and quote `source_location` when citing a specific fact. For that vocab-expansion step, the BFS/DFS traversal modes, the `--budget` cap, the NetworkX fallback, `save-result` feedback, and the `/graphify path` and `/graphify explain` flows, see `references/query.md`.

graphify/skill-copilot.md

@@ -537,14 +537,14 @@ If `--obsidian` was given:
 - If `--obsidian-dir <path>` was also given, pass it via `--dir`. Otherwise defaults to `graphify-out/obsidian`.
 
 ```bash
-graphify export obsidian
-# or with custom dir: graphify export obsidian --dir ~/vaults/my-project
+$(cat graphify-out/.graphify_python) -m graphify export obsidian
+# Add `--dir ~/vaults/my-project` to use a custom directory.
 ```
 
 Generate the HTML graph (always, unless `--no-viz`):
 
 ```bash
-graphify export html  # auto-aggregates to community view if graph > 5000 nodes
+$(cat graphify-out/.graphify_python) -m graphify export html  # auto-aggregates to community view if graph > 5000 nodes
 ```
 
 ### Steps 6b-8 - Wiki, Neo4j, FalkorDB, SVG, GraphML, MCP, benchmark (only on their flags)
@@ -684,7 +684,7 @@ Both are non-default subcommands. `--update` re-extracts only new or changed fil
 When `graphify-out/graph.json` already exists and the user asks a question about the corpus, answer from the graph rather than rebuilding it:
 
 ```bash
-graphify query "<question>"
+$(cat graphify-out/.graphify_python) -m graphify query "<question>"
 ```
 
 Before traversal, expand the question against the graph's own vocabulary so a wording mismatch does not collapse the answer to noise. If the `graphify query` CLI is unavailable, fall back to an inline NetworkX traversal of `graphify-out/graph.json`. Answer using only what the graph output contains, and quote `source_location` when citing a specific fact. For that vocab-expansion step, the BFS/DFS traversal modes, the `--budget` cap, the NetworkX fallback, `save-result` feedback, and the `/graphify path` and `/graphify explain` flows, see `references/query.md`.

graphify/skill-devin.md

@@ -1332,18 +1332,18 @@ from graphify.ingest import ingest
 from pathlib import Path
 
 try:
-    out = ingest('URL', Path('./raw'), author='AUTHOR', contributor='CONTRIBUTOR')
+    out = ingest(sys.argv[1], Path('./raw'), author=sys.argv[2] or None, contributor=sys.argv[3] or None)
     print(f'Saved to {out}')
 except ValueError as e:
     print(f'error: {e}', file=sys.stderr)
     sys.exit(1)
 except RuntimeError as e:
     print(f'error: {e}', file=sys.stderr)
     sys.exit(1)
-"
+" "URL" "AUTHOR" "CONTRIBUTOR"
 ```
 
-Replace `URL` with the actual URL, `AUTHOR` with the user's name if provided, `CONTRIBUTOR` likewise. 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 and pass the user's `AUTHOR` or `CONTRIBUTOR` when provided; use an empty string for either omitted value. After a successful save, automatically run the `--update` pipeline on `./raw` to merge the new file into the existing graph.
 
 Supported URL types (auto-detected):
 - Twitter/X -> fetched via oEmbed, saved as `.md` with tweet text and author

graphify/skill-droid.md

@@ -534,14 +534,14 @@ If `--obsidian` was given:
 - If `--obsidian-dir <path>` was also given, pass it via `--dir`. Otherwise defaults to `graphify-out/obsidian`.
 
 ```bash
-graphify export obsidian
-# or with custom dir: graphify export obsidian --dir ~/vaults/my-project
+$(cat graphify-out/.graphify_python) -m graphify export obsidian
+# Add `--dir ~/vaults/my-project` to use a custom directory.
 ```
 
 Generate the HTML graph (always, unless `--no-viz`):
 
 ```bash
-graphify export html  # auto-aggregates to community view if graph > 5000 nodes
+$(cat graphify-out/.graphify_python) -m graphify export html  # auto-aggregates to community view if graph > 5000 nodes
 ```
 
 ### Steps 6b-8 - Wiki, Neo4j, FalkorDB, SVG, GraphML, MCP, benchmark (only on their flags)
@@ -681,7 +681,7 @@ Both are non-default subcommands. `--update` re-extracts only new or changed fil
 When `graphify-out/graph.json` already exists and the user asks a question about the corpus, answer from the graph rather than rebuilding it:
 
 ```bash
-graphify query "<question>"
+$(cat graphify-out/.graphify_python) -m graphify query "<question>"
 ```
 
 Before traversal, expand the question against the graph's own vocabulary so a wording mismatch does not collapse the answer to noise. If the `graphify query` CLI is unavailable, fall back to an inline NetworkX traversal of `graphify-out/graph.json`. Answer using only what the graph output contains, and quote `source_location` when citing a specific fact. For that vocab-expansion step, the BFS/DFS traversal modes, the `--budget` cap, the NetworkX fallback, `save-result` feedback, and the `/graphify path` and `/graphify explain` flows, see `references/query.md`.

graphify/skill-kilo.md

@@ -537,14 +537,14 @@ If `--obsidian` was given:
 - If `--obsidian-dir <path>` was also given, pass it via `--dir`. Otherwise defaults to `graphify-out/obsidian`.
 
 ```bash
-graphify export obsidian
-# or with custom dir: graphify export obsidian --dir ~/vaults/my-project
+$(cat graphify-out/.graphify_python) -m graphify export obsidian
+# Add `--dir ~/vaults/my-project` to use a custom directory.
 ```
 
 Generate the HTML graph (always, unless `--no-viz`):
 
 ```bash
-graphify export html  # auto-aggregates to community view if graph > 5000 nodes
+$(cat graphify-out/.graphify_python) -m graphify export html  # auto-aggregates to community view if graph > 5000 nodes
 ```
 
 ### Steps 6b-8 - Wiki, Neo4j, FalkorDB, SVG, GraphML, MCP, benchmark (only on their flags)
@@ -684,7 +684,7 @@ Both are non-default subcommands. `--update` re-extracts only new or changed fil
 When `graphify-out/graph.json` already exists and the user asks a question about the corpus, answer from the graph rather than rebuilding it:
 
 ```bash
-graphify query "<question>"
+$(cat graphify-out/.graphify_python) -m graphify query "<question>"
 ```
 
 Before traversal, expand the question against the graph's own vocabulary so a wording mismatch does not collapse the answer to noise. If the `graphify query` CLI is unavailable, fall back to an inline NetworkX traversal of `graphify-out/graph.json`. Answer using only what the graph output contains, and quote `source_location` when citing a specific fact. For that vocab-expansion step, the BFS/DFS traversal modes, the `--budget` cap, the NetworkX fallback, `save-result` feedback, and the `/graphify path` and `/graphify explain` flows, see `references/query.md`.

graphify/skill-kiro.md

@@ -537,14 +537,14 @@ If `--obsidian` was given:
 - If `--obsidian-dir <path>` was also given, pass it via `--dir`. Otherwise defaults to `graphify-out/obsidian`.
 
 ```bash
-graphify export obsidian
-# or with custom dir: graphify export obsidian --dir ~/vaults/my-project
+$(cat graphify-out/.graphify_python) -m graphify export obsidian
+# Add `--dir ~/vaults/my-project` to use a custom directory.
 ```
 
 Generate the HTML graph (always, unless `--no-viz`):
 
 ```bash
-graphify export html  # auto-aggregates to community view if graph > 5000 nodes
+$(cat graphify-out/.graphify_python) -m graphify export html  # auto-aggregates to community view if graph > 5000 nodes
 ```
 
 ### Steps 6b-8 - Wiki, Neo4j, FalkorDB, SVG, GraphML, MCP, benchmark (only on their flags)
@@ -684,7 +684,7 @@ Both are non-default subcommands. `--update` re-extracts only new or changed fil
 When `graphify-out/graph.json` already exists and the user asks a question about the corpus, answer from the graph rather than rebuilding it:
 
 ```bash
-graphify query "<question>"
+$(cat graphify-out/.graphify_python) -m graphify query "<question>"
 ```
 
 Before traversal, expand the question against the graph's own vocabulary so a wording mismatch does not collapse the answer to noise. If the `graphify query` CLI is unavailable, fall back to an inline NetworkX traversal of `graphify-out/graph.json`. Answer using only what the graph output contains, and quote `source_location` when citing a specific fact. For that vocab-expansion step, the BFS/DFS traversal modes, the `--budget` cap, the NetworkX fallback, `save-result` feedback, and the `/graphify path` and `/graphify explain` flows, see `references/query.md`.

graphify/skill-opencode.md

@@ -529,14 +529,14 @@ If `--obsidian` was given:
 - If `--obsidian-dir <path>` was also given, pass it via `--dir`. Otherwise defaults to `graphify-out/obsidian`.
 
 ```bash
-graphify export obsidian
-# or with custom dir: graphify export obsidian --dir ~/vaults/my-project
+$(cat graphify-out/.graphify_python) -m graphify export obsidian
+# Add `--dir ~/vaults/my-project` to use a custom directory.
 ```
 
 Generate the HTML graph (always, unless `--no-viz`):
 
 ```bash
-graphify export html  # auto-aggregates to community view if graph > 5000 nodes
+$(cat graphify-out/.graphify_python) -m graphify export html  # auto-aggregates to community view if graph > 5000 nodes
 ```
 
 ### Steps 6b-8 - Wiki, Neo4j, FalkorDB, SVG, GraphML, MCP, benchmark (only on their flags)
@@ -676,7 +676,7 @@ Both are non-default subcommands. `--update` re-extracts only new or changed fil
 When `graphify-out/graph.json` already exists and the user asks a question about the corpus, answer from the graph rather than rebuilding it:
 
 ```bash
-graphify query "<question>"
+$(cat graphify-out/.graphify_python) -m graphify query "<question>"
 ```
 
 Before traversal, expand the question against the graph's own vocabulary so a wording mismatch does not collapse the answer to noise. If the `graphify query` CLI is unavailable, fall back to an inline NetworkX traversal of `graphify-out/graph.json`. Answer using only what the graph output contains, and quote `source_location` when citing a specific fact. For that vocab-expansion step, the BFS/DFS traversal modes, the `--budget` cap, the NetworkX fallback, `save-result` feedback, and the `/graphify path` and `/graphify explain` flows, see `references/query.md`.

graphify/skill-pi.md

@@ -537,14 +537,14 @@ If `--obsidian` was given:
 - If `--obsidian-dir <path>` was also given, pass it via `--dir`. Otherwise defaults to `graphify-out/obsidian`.
 
 ```bash
-graphify export obsidian
-# or with custom dir: graphify export obsidian --dir ~/vaults/my-project
+$(cat graphify-out/.graphify_python) -m graphify export obsidian
+# Add `--dir ~/vaults/my-project` to use a custom directory.
 ```
 
 Generate the HTML graph (always, unless `--no-viz`):
 
 ```bash
-graphify export html  # auto-aggregates to community view if graph > 5000 nodes
+$(cat graphify-out/.graphify_python) -m graphify export html  # auto-aggregates to community view if graph > 5000 nodes
 ```
 
 ### Steps 6b-8 - Wiki, Neo4j, FalkorDB, SVG, GraphML, MCP, benchmark (only on their flags)
@@ -684,7 +684,7 @@ Both are non-default subcommands. `--update` re-extracts only new or changed fil
 When `graphify-out/graph.json` already exists and the user asks a question about the corpus, answer from the graph rather than rebuilding it:
 
 ```bash
-graphify query "<question>"
+$(cat graphify-out/.graphify_python) -m graphify query "<question>"
 ```
 
 Before traversal, expand the question against the graph's own vocabulary so a wording mismatch does not collapse the answer to noise. If the `graphify query` CLI is unavailable, fall back to an inline NetworkX traversal of `graphify-out/graph.json`. Answer using only what the graph output contains, and quote `source_location` when citing a specific fact. For that vocab-expansion step, the BFS/DFS traversal modes, the `--budget` cap, the NetworkX fallback, `save-result` feedback, and the `/graphify path` and `/graphify explain` flows, see `references/query.md`.