Replace the misleading .claudeignore troubleshooting entry (#1843)

[ayushcodes10]

Summary

Fixes #1843. The README's prompt-cache troubleshooting entry told users to add `graph.json`/`graphify-out/` to a `.claudeignore` file to stop Claude Code's prompt cache from invalidating on every write. Claude Code never shipped `.claudeignore` support — the original feature request (anthropics/claude-code#579) was closed in favor of `permissions.deny` rules, and a long tail of user reports confirms the file is silently ignored when present. The README's remedy is a no-op: users create the file, nothing changes, and the symptom persists.

Fix

Replaced with the supported mechanism:
```json
// .claude/settings.json
{ "permissions": { "deny": ["Read(./graphify-out/**)", "Read(./graph.json)"] } }
```
Added a note that this trades off against the wiki-as-navigation workflow (`export wiki`, `graphify-out/wiki/`), since a deny rule also blocks reading those files, not just writes.

Test plan

• Docs-only change; no code paths affected. Confirmed no test pins the old `.claudeignore` text.
• Full suite: `python3 -m pytest -q` — 5621 passed, 68 skipped, no regressions.

🤖 Generated with Claude Code

[graphify-labs]

Graphify reviewed this change.

Looks safe to merge — no coupling regressions and no blocking issues, checked against the code graph (not a self-assessment).

---

Graphify review — findings

Corrects the prompt-cache troubleshooting guidance in the README to use permissions.deny in .claude/settings.json instead of the non-existent .claudeignore, since Claude Code never shipped .claudeignore support and the old advice was a no-op. Adds a note that the deny rule also blocks reading graph.json/graphify-out/, so it conflicts with the wiki-as-navigation workflow. Records both in the changelog under 0.9.63.

No blocking issues surfaced.

Analysis details — impact, health, verification

Impact & health

Graphify review

Impact — 235 functions depend on the 235 functions this change touches.

Health — grade A; no new coupling hotspots.

Verification — 235 functions in the blast radius were not formally verified this run (proofs are advisory here).

Gate & verification

graphify gate

PASS — objectively clean (no health regressions, tests not run — proofs not run this pass (advisory)). Grounded, not self-assessed.

Advisory (not blocking):

• verification_scope: 235 function(s) in the blast radius were not formally verified this run

Test selection

Test selection

286 of 286 test file(s) selected (100%) via static blast radius.

Escalated to a full run for safety — the selection is not trustworthy on its own (see below). CI should run the whole suite.

• tests/test_affected_cli.py — full-run-safety
• tests/test_affected_member_seed.py — full-run-safety
• tests/test_agents_platform.py — full-run-safety
• tests/test_analyze.py — full-run-safety
• tests/test_anthropic_custom_endpoint.py — full-run-safety
• tests/test_antigravity_install.py — full-run-safety
• tests/test_apm_fallback_version.py — full-run-safety
• tests/test_architecture_doc.py — full-run-safety
• tests/test_astro_extraction.py — full-run-safety
• tests/test_astro_import_ids.py — full-run-safety
• tests/test_atomic_canvas_export.py — full-run-safety
• tests/test_atomic_version_stamp.py — full-run-safety
• tests/test_atomic_writes.py — full-run-safety
• tests/test_backend_env_isolation.py — full-run-safety
• tests/test_backend_extras.py — full-run-safety
• tests/test_benchmark.py — full-run-safety
• tests/test_benchmark_raw_graph.py — full-run-safety
• tests/test_build.py — full-run-safety
• tests/test_build_merge_dedup_scope.py — full-run-safety
• tests/test_build_merge_hyperedges_and_prune.py — full-run-safety
• tests/test_build_merge_shrink_guard.py — full-run-safety
• tests/test_builtin_global_type_refs.py — full-run-safety
• tests/test_cache.py — full-run-safety
• tests/test_callflow_html.py — full-run-safety
• tests/test_cargo_introspect.py — full-run-safety
• tests/test_carried_hyperedge_remap.py — full-run-safety
• tests/test_case_sensitive_resolution.py — full-run-safety
• tests/test_charmap_encoding.py — full-run-safety
• tests/test_chunking.py — full-run-safety
• tests/test_cjs_module_extension.py — full-run-safety
• tests/test_claude_cli_backend.py — full-run-safety
• tests/test_claude_md.py — full-run-safety
• tests/test_cli_broken_pipe.py — full-run-safety
• tests/test_cli_export.py — full-run-safety
• tests/test_cli_help.py — full-run-safety
• tests/test_cluster.py — full-run-safety
• tests/test_codebuddy.py — full-run-safety
• tests/test_community_hub_labels.py — full-run-safety
• tests/test_community_labels_skill.py — full-run-safety
• tests/test_confidence.py — full-run-safety
• tests/test_corrupt_graph_json.py — full-run-safety
• tests/test_cpp_nested_and_cli.py — full-run-safety
• tests/test_cpp_objc_cross_file_calls.py — full-run-safety
• tests/test_cpp_preprocess.py — full-run-safety
• tests/test_cross_extension_reexport_self_cycle.py — full-run-safety
• tests/test_cross_language_call_resolution.py — full-run-safety
• tests/test_cross_repo_external_call_guards.py — full-run-safety
• tests/test_cross_repo_member_calls.py — full-run-safety
• tests/test_cross_repo_shared_types.py — full-run-safety
• tests/test_csharp_call_site_generic_args.py — full-run-safety
• … and 236 more

non-code file(s) changed (CHANGELOG.md, README.md) → running the full suite for safety (a code graph can't see config/fixture/data deps)

changed code file(s) with no mapped test (CHANGELOG.md, README.md) — a coverage gap or a missing link — running the full suite rather than only the selected tests

Selection is safe under the controlled-regression assumption; always-run tests + a periodic full run are the backstops. Advisory — it never changes the check verdict.