Bug: `--fix` unexpectedly removes eslint-disable comment

[andersk]

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• [X] I have tried restarting my IDE and the issue persists.
• [X] I have updated to the latest version of the packages.
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Issue Description

typescript-eslint correctly flags a @typescript-eslint/no-unsafe-member-access error when accessing an untyped module.

However, if I ignore this error with an eslint-disable-next-line comment, and reportUnusedDisableDirectives is enabled, the comment is unexpectedly removed by eslint --fix.

With the comment removed, the error is not reported when running with --fix, but it is reported when running without --fix.

Reproduction Repository Link

https://gist.github.com/andersk/5bacfa857d080e6ed6627063f0700694

Repro Steps

$ git clone https://gist.github.com/andersk/5bacfa857d080e6ed6627063f0700694 test
$ cd test
$ npm i
$ npx eslint test.ts
$ npx eslint --fix test.ts
$ git diff
diff --git a/test.ts b/test.ts
index 533595b..049fb4d 100644
--- a/test.ts
+++ b/test.ts
@@ -1,5 +1,5 @@
 // @ts-expect-error This module is not typed
 import * as untyped from "./untyped";
 
-// eslint-disable-next-line @typescript-eslint/no-unsafe-member-access
+ 
 console.log(untyped.hello);
$ npx eslint test.ts
/tmp/test/test.ts
  5:21  error  Unsafe member access .hello on an `error` typed value  @typescript-eslint/no-unsafe-member-access

✖ 1 problem (1 error, 0 warnings)

Versions

package	version
@typescript-eslint/eslint-plugin	8.6.0
@typescript-eslint/parser	8.6.0
@typescript-eslint/scope-manager	8.6.0
@typescript-eslint/typescript-estree	8.6.0
@typescript-eslint/type-utils	8.6.0
@typescript-eslint/utils	8.6.0
TypeScript	5.5.4
ESLint	9.10.0
node	20.17.0

[kirkwaiblinger]

Confirmed locally.... weird!

wondering if it's to do with single run inference related things? Note that the report also shows up as unused in my editor.

[auvred]

Running eslint test.ts without --fix implies: single run === true -> TS programs are created from tsconfig.json specified in eslint.config.mjs https://github.com/typescript-eslint/typescript-eslint/blob/2055cfbbdef5d9b7ee4ed7180f0af93eed245235/packages/typescript-estree/src/parser.ts#L168-L196 Running eslint --fix test.ts implies: single run === false -> create watch program -> create watch compiler host -> watch compiler host created with allowJs: true since it is set as the default compiler option https://github.com/typescript-eslint/typescript-eslint/blob/2055cfbbdef5d9b7ee4ed7180f0af93eed245235/packages/typescript-estree/src/create-program/shared.ts#L34-L52

In the second case (with --fix), the TS program allows importing .js files. Therefore, untyped.hello is not reported as an "error typed value".

---

optionsToExtend (containing allowJs: true) passed to watch compiler host will take precedence over compiler options from the project: 'tsconfig.json' specified. Even if user specified "allowJs": false, importing JS will be allowed during eslint file.ts run. I think we should exclude allowJs from watch compiler host options. WDYT?

---

A very similar issue was reported in some repositories after single run inference was enabled by default: https://github.com/typescript-eslint/typescript-eslint/issues/9749