fix: avoid write-on-read mutation of config file (#11940)

* fix: avoid write-on-read mutation of config file

* fix: update test description for schema injection case

* Apply suggestion from @kilo-code-bot[bot]

Co-authored-by: kilo-code-bot[bot] <240665456+kilo-code-bot[bot]@users.noreply.github.com>

* chore: add changeset

* fix(cli): preserve  as first config property via getInsertionIndex

* fix(cli): close missing brackets in config test preventing syntax error

* Removed test for preserving environment variables when adding $schema to config.

Removed test for preserving environment variables when adding $schema to config.

* fix(cli): add  ordering assertions to existing injection tests

* docs(changeset): clarify per-load churn scope for comment-first JSONC

* test(cli): use FSUtil in config schema tests after upstream refactor

* chore: combine changeset lines

---------

Co-authored-by: kilo-code-bot[bot] <240665456+kilo-code-bot[bot]@users.noreply.github.com>

.changeset/config-schema-injection-jsonc.md

@@ -0,0 +1,5 @@
+---
+"@kilocode/cli": patch
+---
+
+Fix: inject `$schema` into config files using jsonc-parser, avoiding write-on-read for comment-first JSONC and preventing unnecessary file rewrites on every load

packages/opencode/src/config/config.ts

@@ -319,9 +319,15 @@ export const layer = Layer.effect(
       if (!data.$schema) {
         // kilocode_change start
         data.$schema = "https://app.kilo.ai/config.json"
-        const updated = text.replace(/^\s*\{/, '{\n  "$schema": "https://app.kilo.ai/config.json",')
+        const edits = modify(text, ["$schema"], "https://app.kilo.ai/config.json", {
+          formattingOptions: { insertSpaces: true, tabSize: 2 },
+          getInsertionIndex: () => 0,
+        })
+        const updated = applyEdits(text, edits)
+        if (updated !== text) {
+          yield* fs.writeFileString(options.path, updated).pipe(Effect.catch(() => Effect.void))
+        }
         // kilocode_change end
-        yield* fs.writeFileString(options.path, updated).pipe(Effect.catch(() => Effect.void))
       }
       return data
     })

packages/opencode/test/config/config.test.ts

@@ -578,6 +578,68 @@ it.instance("rejects environment variable substitution in project config", () =>
   ),
 )
 
+it.instance("injects $schema into config without existing schema", () =>
+  Effect.gen(function* () {
+    const test = yield* TestInstance
+    // Config without $schema - should trigger auto-add
+    yield* FSUtil.use.writeWithDirs(
+      path.join(test.directory, "kilo.json"),
+      JSON.stringify({ username: "test-user" }),
+    )
+    const config = yield* Config.use.get()
+    expect(config.username).toBe("test-user")
+    expect(config.$schema).toBe("https://app.kilo.ai/config.json")
+
+    // Read the file to verify $schema was injected
+    const content = yield* FSUtil.use.readFileString(path.join(test.directory, "kilo.json"))
+    expect(content).toContain('"$schema": "https://app.kilo.ai/config.json"')
+    const schemaIndex = content.indexOf('"$schema"')
+    const usernameIndex = content.indexOf('"username"')
+    expect(schemaIndex).toBeLessThan(usernameIndex)
+  }),
+)
+
+it.instance("injects $schema into comment-first JSONC config", () =>
+  Effect.gen(function* () {
+    const test = yield* TestInstance
+    // Config with leading comment - regex-based injection would fail
+    yield* FSUtil.use.writeWithDirs(
+      path.join(test.directory, "kilo.jsonc"),
+      '// project config\n{\n  "model": "test/model"\n}\n',
+    )
+    const config = yield* Config.use.get()
+    expect(config.model).toBe("test/model")
+    expect(config.$schema).toBe("https://app.kilo.ai/config.json")
+
+    // Read the file to verify $schema was injected correctly
+    const content = yield* FSUtil.use.readFileString(path.join(test.directory, "kilo.jsonc"))
+    expect(content).toContain('"$schema": "https://app.kilo.ai/config.json"')
+    expect(content).toContain("// project config")
+    const schemaIndex = content.indexOf('"$schema"')
+    const modelIndex = content.indexOf('"model"')
+    expect(schemaIndex).toBeLessThan(modelIndex)
+  }),
+)
+
+it.instance("does not write config when $schema already present", () =>
+  Effect.gen(function* () {
+    const test = yield* TestInstance
+    const filepath = path.join(test.directory, "kilo.json")
+    // Config already has $schema - should not rewrite file
+    yield* FSUtil.use.writeWithDirs(
+      filepath,
+      JSON.stringify({ $schema: "https://app.kilo.ai/config.json", username: "test-user" }),
+    )
+    const before = yield* Effect.promise(() => fs.stat(filepath))
+
+    const config = yield* Config.use.get()
+    expect(config.username).toBe("test-user")
+
+    const after = yield* Effect.promise(() => fs.stat(filepath))
+    expect(after.mtimeMs).toBe(before.mtimeMs)
+  }),
+)
+
 it.instance("allows {file:} that stays inside the project root", () =>
   Effect.gen(function* () {
     const test = yield* TestInstance