docs: fix Claude Code prompt-cache troubleshooting — .claudeignore is a no-op, use .claude/settings.json deny rules

[prvthmpcypher]

Fixes #1843

Problem

The Troubleshooting section advised users to add graph.json and
graphify-out/ to a .claudeignore file to prevent Claude Code's prompt
cache from being invalidated on every graphify extract run.

.claudeignore does not exist in Claude Code. Evidence from the issue:

• The official Claude Code docs document permissions.deny Read rules
  (in .claude/settings.json) as the supported mechanism, replacing the
  deprecated ignorePatterns. No page mentions .claudeignore.
• The original .claudeignore feature request
  (anthropic/claude-code#579) was closed with "you can do this now with
  deny permission rules" — no .claudeignore file was ever shipped.
• Multiple user bug reports confirm the file silently does nothing
  (anthropic/claude-code#36163, #16704, #46699, #56997, #65812).

So users following the README created a file that had no effect, and the
prompt-cache symptom persisted.

Fix

Replaced the .claudeignore block with the supported equivalent —
a deny rule in .claude/settings.json — and added a plain-language
note explaining the tradeoff: deny rules gate Claude Code's read
access, not just cache inclusion, which means Claude Code can no longer
read GRAPH_REPORT.md, the wiki, or other files under graphify-out/.
Users who rely on those files for navigation need to know this before
applying the fix.

Changes

README.md — Troubleshooting section, "Claude Code prompt cache
invalidated after every graphify extract":

• Removed the .claudeignore code block
• Added the correct .claude/settings.json deny rule
• Added a note about the access-vs-cache tradeoff and the option to
  scope the rule to specific files only