custom_lint throws PathNotFoundException in pnpm workspace

[BuyMyBeard]

Describe the bug
I have a monorepo with a bunch of packages written in TS. At the root is the Flutter front-end project and a node_modules for pnpm dependencies. It is oddly specific, but if I have the npm firebase package installed through pnpm, and I run dart run custom_lint, the following exception is thrown:

Exception

W:\DevXpress\custom_lint_issue_repro> dart run custom_lint
Building package executable... 
Built custom_lint:custom_lint.
PathNotFoundException: Directory listing failed, path = 'W:\DevXpress\custom_lint_issue_repro\node_modules\.pnpm\@firebase+firestore-compat@0.3.39_@firebase+app-compat@0.2.45_@firebase+app-types@0.9.2_@firebase+app@0.10.15\node_modules\@firebase\firestore\dist\firestore\test\unit\remote\bloom_filter_golden_test_data\*' (OS Error: The system cannot find the path specified.
, errno = 3)
#0      _Directory._fillWithDirectoryListing (dart:io-patch/directory_patch.dart:42:24)
#1      _Directory.listSync (dart:io/directory_impl.dart:228:5)
#2      _findRoots (package:custom_lint/src/workspace.dart:411:20)
#3      _SyncStarIterator.moveNext (dart:async-patch/async_patch.dart:560:14)
#4      ExpandIterator.moveNext (dart:_internal/iterable.dart:487:32)
#5      SetBase.addAll (dart:collection/set.dart:58:23)
#6      _Set.addAll (dart:collection-patch/compact_hash.dart:986:11)
#7      new LinkedHashSet.of (dart:collection/linked_hash_set.dart:192:27)
#8      Iterable.toSet (dart:core/iterable.dart:513:21)
#9      CustomLintWorkspace.fromPaths (package:custom_lint/src/workspace.dart:440:10)
#10     _runServer.<anonymous closure> (package:custom_lint/custom_lint.dart:90:51)
#11     CustomLintServer.runZoned.<anonymous closure> (package:custom_lint/src/v2/custom_lint_analyzer_plugin.dart:80:17)
#12     new Future.<anonymous closure> (dart:async/future.dart:258:40)
#13     _rootRun (dart:async/zone.dart:1391:47)
#14     _CustomZone.run (dart:async/zone.dart:1301:19)
#15     _CustomZone.runGuarded (dart:async/zone.dart:1209:7)
#16     _CustomZone.bindCallbackGuarded.<anonymous closure> (dart:async/zone.dart:1249:23)
#17     _rootRun (dart:async/zone.dart:1399:13)
#18     _CustomZone.run (dart:async/zone.dart:1301:19)
#19     _CustomZone.bindCallback.<anonymous closure> (dart:async/zone.dart:1233:23)
#20     Timer._createTimer.<anonymous closure> (dart:async-patch/timer_patch.dart:18:15)
#21     _Timer._runTimers (dart:isolate-patch/timer_impl.dart:398:19)
#22     _Timer._handleMessage (dart:isolate-patch/timer_impl.dart:429:5)
#23     _RawReceivePort._handleMessage (dart:isolate-patch/isolate_patch.dart:184:12)

I find this oddly specific, because I couldn't reproduce the issue by installing the same dependency through npm install instead, or installing a different package through pnpm.

I have tried to exclude node_modules from analysis_options.yaml, but to no avail. It feels nonsensical for custom_lint to try and go lint node_modules.

I am also under the impression this causes some slowdowns to static analysis, but I have not tested it.

To Reproduce

I set up a minimal reproductible example at the following link. Steps for setup are in the readme.

Expected behavior
Able to run dart run custom_lint in pnpm workspace