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docs: replace unsupported .claudeignore with permissions.deny rules#1877

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Yashasm18:fix/readme-claudeignore-deny-rules
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docs: replace unsupported .claudeignore with permissions.deny rules#1877
Yashasm18 wants to merge 1 commit into
Graphify-Labs:v8from
Yashasm18:fix/readme-claudeignore-deny-rules

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Fixes #1843.

The README's troubleshooting section recommended adding .claudeignore
to prevent graph.json/graphify-out/ from invalidating Claude Code's
prompt cache. Claude Code doesn't read .claudeignore, so this was a
no-op — users following it saw no change.

Replaced it with the supported permissions.deny Read rules in
.claude/settings.json, and added a note that deny rules gate access
(not just cache visibility), which conflicts with workflows that browse
graphify-out/ as a navigable wiki.

Claude Code does not read .claudeignore; the previous remedy was a no-op.
Document the supported permissions.deny approach and the access trade-off.

Fixes Graphify-Labs#1843
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README troubleshooting recommends .claudeignore, which Claude Code does not support

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