Commands in symlinked .claude directory skipped as duplicates since v2.1.30 (Windows + network drive)

Bug Description

Since v2.1.30, custom slash commands in a symlinked ~/.claude directory are skipped as duplicates on Windows. Only the first command (alphabetically) is loaded; all others are silently dropped with "same inode already loaded from userSettings".

This is a regression introduced by the 64-bit inode precision fix in v2.1.30.

Environment

• Claude Code version: 2.1.37
• OS: Windows 11
• Setup: C:\Users\<user>\.claude is a symlink to X:\.claude (SMB network share mapped drive)

Root Cause

Claude Code scans ~/.claude/commands/ twice:

1. Via the symlink path: C:\Users\<user>\.claude\commands\
2. Via the resolved realpath: X:\.claude\commands\

Both paths point to the same physical directory. After the v2.1.30 inode precision improvement, the deduplication logic correctly detects identical inodes — but incorrectly skips files that were discovered through the same directory via two different paths.

// realpathSync resolves symlink to different path
C:\Users\<user>\.claude  →  symlink  →  X:\.claude
realpathSync('C:/Users/<user>/.claude') === 'X:\.claude'  // different string, same directory

Debug Log Evidence

[DEBUG] Loading skills from: managed=C:\ProgramData\ClaudeCode\.claude\skills, user=C:\Users\<user>\.claude\skills, project=[]
[DEBUG] [STARTUP] Loading commands and agents...
[DEBUG] Skipping duplicate file 'C:\Users\<user>\.claude\commands\build.md' from userSettings (same inode already loaded from userSettings)
[DEBUG] Skipping duplicate file 'C:\Users\<user>\.claude\commands\debug.md' from userSettings (same inode already loaded from userSettings)
[DEBUG] Skipping duplicate file 'C:\Users\<user>\.claude\commands\expert.md' from userSettings (same inode already loaded from userSettings)
[DEBUG] Skipping duplicate file 'C:\Users\<user>\.claude\commands\test.md' from userSettings (same inode already loaded from userSettings)
... (all files except the first one alphabetically)

Only analyze.md (first alphabetically) is loaded. All other commands return "Unknown skill".

Reproduction Steps

1. On Windows, create a symlink from ~/.claude to a network share (SMB):

``powershell
mklink /D C:\Users\<user>\.claude X:\.claude
``

1. Place multiple .md files in .claude/commands/
2. Run claude and try /build or any command other than the alphabetically first one
3. Result: Unknown skill: build

Expected Behavior

All commands in ~/.claude/commands/ should be loaded regardless of whether the directory is accessed via symlink or realpath. The deduplication should compare normalized paths or skip re-scanning when the resolved path is the same directory.

Suggested Fix

Before scanning commands, normalize the paths so that symlink path and realpath are recognized as the same source:

// Instead of scanning both the symlink path and realpath separately,
// resolve once and scan only the resolved path
const commandsDir = fs.realpathSync(path.join(homeDir, '.claude', 'commands'));
// scan commandsDir only once

Or deduplicate by resolved path rather than by inode across different scan passes of the same settings level.

Workaround

Remove the symlink and use a local .claude directory (loses sync between machines).

Additional Context

• This worked correctly on v2.1.29 and earlier because float-precision inode comparison didn't detect the duplicates
• The same .claude directory works perfectly on Linux (local filesystem, no symlink needed)
• node -e "fs.realpathSync('C:/Users/<user>/.claude')" returns X:\.claude, confirming the symlink resolution causes the path mismatch