fix(installer): preserve comments and key order when editing agent configs

Cargo.toml

@@ -55,6 +55,9 @@ notify = "6"
 # CLI
 clap = { version = "4.5", features = ["derive"] }
 
+# JSONC config editing (preserve comments + key order on agent config writes)
+jsonc-parser = { version = "0.26", features = ["cst", "serde"] }
+
 # Benchmarking
 criterion = "0.7"
 

README.md

@@ -399,7 +399,7 @@ golden byte-stable output.
   layer — see above).
 - No semantic search; search is FTS5 + deterministic scoring only.
 - Concrete `FrameworkResolver`s exist for React/Vue/NestJS; other framework
-  resolution is deferred (see [`KNOWN_DIFFS.md`](KNOWN_DIFFS.md)).
+  resolution is deferred.
 - No languages beyond the fixed `LANGUAGES` set.
 
 ---
@@ -415,8 +415,6 @@ golden byte-stable output.
 - [`docs/grammar-manifest.md`](docs/grammar-manifest.md) /
   [`docs/embedded-extraction.md`](docs/embedded-extraction.md) — languages /
   extraction.
-- [`KNOWN_DIFFS.md`](KNOWN_DIFFS.md) — registered Tier-3 presentation diffs (read
-  at runtime by the equivalence oracle).
 - [`examples/`](examples/) — codegraph -> LLM orchestration example.
 - [`docs/readme/README.zh-CN.md`](docs/readme/README.zh-CN.md) — 中文说明.
 

crates/codegraph-cli/Cargo.toml

@@ -27,6 +27,7 @@ codegraph-store = { path = "../codegraph-store", version = "0.1.0" }
 codegraph-watch = { path = "../codegraph-watch", version = "0.1.0" }
 serde = { workspace = true }
 serde_json = { workspace = true }
+jsonc-parser = { workspace = true }
 toml = { workspace = true }
 anyhow = { workspace = true }
 clap = { workspace = true }