[Bug]: Skill suggests --force on a refused shrink but never passes force=True to to_json() #4777

Pre-flight checks

• I have checked the Troubleshooting section in the README

What happened?

When to_json() refuses to shrink graph.json (#479 shrink guard), the generated skill prints:

If this shrink is intentional (you deleted files), re-run a full build with --force.

Neither export in the skill passes force=True, although to_json(..., *, force=False) supports it:

• Step 4: wrote = to_json(G, communities, 'graphify-out/graph.json')
• Step 5 (re-export with community labels): wrote = to_json(G, communities, 'graphify-out/graph.json', community_labels=labels)

Source fragment on v8: tools/skillgen/fragments/core/core.md (lines 434 and 521 at 92741d1).

Following the advice therefore hits the same refusal, and the skill has no working recovery path for an intentional shrink (other than deleting graphify-out/graph.json by hand).

Expected: keep the shrink guard by default, and pass force=True to both exports only when the user explicitly invoked the skill with --force.

Steps to reproduce

mkdir repro && cd repro && mkdir graphify-out
python -c "
import networkx as nx
from graphify.export import to_json
big = nx.Graph()
for i in range(50): big.add_node(f'n{i}', label=f'n{i}', source_file=f'f{i}.py', file_type='code')
print('first write:', to_json(big, {0: list(big.nodes)}, 'graphify-out/graph.json'))
small = nx.Graph()
for i in range(10): small.add_node(f'n{i}', label=f'n{i}', source_file=f'f{i}.py', file_type='code')
--force
print('skill Step 4 write:', to_json(small, {0: list(small.nodes)}, 'graphify-out/graph.json'))
print('with force=True:', to_json(small, {0: list(small.nodes)}, 'graphify-out/graph.json', force=True))
"

Error output or graph output

[graphify] WARNING: Refusing to overwrite — saved semantic node(s) are missing from the new graph: n10, n11, ..., n49.
first write: True
skill Step 4 write: False
with force=True: True

Graphify version

0.9.95

Operating System

macOS

Python Version

3.13

Installation Method

uv tool install (recommended)

Additional Environment Details

Python 3.14.10 from the uv tool environment. No provider environment variables set. Reproduced in a fresh empty directory.

Additional context

Related but different: #2833 (update --force reporting), #2976 (graphify label path), #2436 (cluster-only success message when to_json refuses).