fix(installer): preserve comments and key order when editing agent configs - #9
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…nfigs The installer rewrote agent config files with serde_json::to_string_pretty, which dropped all JSONC comments and re-sorted keys alphabetically — scrambling users' hand-maintained configs even when only adding the codegraph entry. Edit existing configs surgically with jsonc-parser's CST API (upsert_nested_key_jsonc / remove_nested_key_jsonc): only the codegraph property is inserted, updated, or removed, leaving every comment, key order, and the file's formatting intact. Re-runs short-circuit to Unchanged (no churn). Fresh files are still seeded with the canonical shape. All six targets and the uninstall path go through the surgical helpers.
KNOWN_DIFFS.md is an internal upstream-diff ledger (deferred colby resolvers, Tier-3 allowed diffs), not user-facing. No code loads it at runtime. Move it under docs/upstream-sync/ (already gitignored, alongside UPSTREAM.md) so it stays local and out of the public repo.
KNOWN_DIFFS.md moved to the internal gitignored ledger, so its public-doc hyperlinks would 404. Delink the mentions in README, architecture.md, and the zh-CN README; also drop the inaccurate 'read at runtime by the equivalence oracle' claim (no code loads the file by path).
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Summary
The installer rewrote agent config files with serde_json::to_string_pretty, which dropped all JSONC comments and re-sorted keys alphabetically, scrambling users' hand-maintained configs even when only adding the codegraph entry.
Fix
upsert_nested_key_jsonc/remove_nested_key_jsonc): only the codegraph property is inserted/updated/removed; every comment, key order, and the file formatting stay intact.Verification