fix(core): silently skip GEMINI.md paths that are directories (EISDIR)

[martin-hsu-test]

Summary

When a directory named GEMINI.md exists anywhere in the workspace tree, memory discovery currently surfaces a confusing Could not read GEMINI.md warning because fs.readFile throws EISDIR on directories. Directories with that name are valid in some project structures and should simply be ignored.

This PR detects EISDIR specifically in the readGeminiMdFiles catch block and skips silently with a debug log, while preserving the warning behaviour for genuinely unexpected read errors.

Fixes #16282

Implementation

packages/core/src/utils/memoryDiscovery.ts — extend the existing catch block:

const isEISDIR =
  error instanceof Error &&
  (error as NodeJS.ErrnoException).code === 'EISDIR';

if (isEISDIR) {
  // Skip silently — a directory at this path is a legitimate case.
  debugLogger.debug('[DEBUG] [MemoryDiscovery] Skipping directory at GEMINI.md path:', filePath);
} else {
  // ... existing warn behaviour ...
}

The return value is unchanged ({ filePath, content: null }) so downstream consumers continue to see the same shape.

Tests

Two new tests in memoryDiscovery.test.ts:

1. Direct unit test — readGeminiMdFiles returns { content: null } (without throwing) when given a directory path
2. End-to-end test — loadServerHierarchicalMemory returns empty memory when a GEMINI.md directory exists in the workspace

Test results:

✓ packages/core/src/utils/memoryDiscovery.test.ts (44 tests) 107ms
Test Files  1 passed (1)
     Tests  44 passed (44)

tsc --noEmit and eslint both pass with zero output.

Relationship to #22852

This supersedes #22852 (closed 2026-04-09 due to test failures and 23 days of inactivity). Credit to @shathwik30 for the original work; the production-code shape here uses the same NodeJS.ErrnoException type guard that @gemini-code-assist suggested on that PR.

What's different in this PR:

• Tests are written from scratch against the current memoryDiscovery.ts and verified to pass locally before submission
• Added a direct readGeminiMdFiles unit test (alongside the e2e test) to keep the failure surface narrow and easy to debug for future contributors
• The end-to-end test asserts only memoryContent === '', which is the user-visible contract the issue actually cares about, rather than relying on fileCount semantics that could shift

[gemini-code-assist]

Summary of Changes

Hello, I'm Gemini Code Assist¹! I'm currently reviewing this pull request and will post my feedback shortly. In the meantime, here's a summary to help you and other reviewers quickly get up to speed!

This pull request addresses an issue where the memory discovery process incorrectly flagged directories named GEMINI.md as read errors. By identifying the EISDIR error code during file reading, the system now treats these directories as expected edge cases rather than failures, improving the user experience by removing unnecessary warnings.

Highlights

• Error Handling: Updated the readGeminiMdFiles function to explicitly catch and silently ignore EISDIR errors, preventing misleading warnings when a directory is named GEMINI.md.
• Testing: Added comprehensive unit and end-to-end tests to verify that GEMINI.md directories are handled gracefully without throwing errors.

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[gemini-code-assist]

Code Review

This pull request introduces graceful handling for cases where a directory exists at a path expected to be a GEMINI.md file. The readGeminiMdFiles function in packages/core now specifically catches EISDIR errors, logging a debug message instead of a warning to prevent user confusion. Additionally, new test cases have been added to memoryDiscovery.test.ts to verify that these directories are correctly ignored without throwing exceptions. I have no feedback to provide.

[martin-hsu-test]

Pushed a follow-up commit (1236565) adding two tests that cover the broader contract from the issue:

• Fallback to actual files: when a higher-level GEMINI.md is a real file but a lower-level path of the same name is a directory, the real file is still discovered and loaded. This validates the 'ignored in favor of actual files' wording in [Core] Handle EISDIR error when GEMINI.md is a directory during memory discovery #16282.
• Symlink to directory: a symlink whose target is a directory triggers the same EISDIR path on read and is skipped silently, validating the 'handles symlinks more robustly' point. The test self-skips on Windows setups without symlink-creation privilege.

All 46 memoryDiscovery tests still pass locally; lint clean.