[Bug] CLAUDE.md loaded twice when multiple junction links point to the same directory on Windows

[jaried]

Bug Description

When using Windows junction links (mklink /J) to create multiple symlinks pointing to the same .claude directory, Claude Code loads the global CLAUDE.md file multiple times — once for each junction link path — instead of deduplicating by real path.

Environment

• Claude Code version: 2.1.45
• Subscription: Max 5
• OS: Windows 10
• Terminal: Windows Terminal

Setup

I have two junction links both pointing to the same physical directory:

C:\Users\Tony\.claude  →  D:\Tony\ubuntu_settings\.claude\  (mklink /J)
D:\Tony\.claude        →  D:\Tony\ubuntu_settings\.claude\  (mklink /J)

Both symlinks resolve to the same underlying directory D:\Tony\ubuntu_settings\.claude.

Observed Behavior

Running /context shows the global CLAUDE.md loaded twice, consuming ~20k tokens:

Memory files
└ C:\Users\Tony\.claude\CLAUDE.md: 10.1k tokens
└ D:\Tony\.claude\CLAUDE.md: 10.1k tokens

Expected Behavior

Claude Code should resolve junction links / symlinks to their real path before loading memory files. Duplicate real paths should only be loaded once:

Memory files
└ D:\Tony\ubuntu_settings\.claude\CLAUDE.md: 10.1k tokens

Impact

• ~10k tokens wasted per conversation due to duplicate loading
• In a 200k context window, this represents ~5% waste from a single duplicated file
• Users with junction links on Windows are silently penalized

Suggested Fix

Before loading CLAUDE.md files, resolve each candidate path to its real/canonical path (e.g., using fs.realpathSync on Node.js). Deduplicate by real path before loading.

Workaround

None currently available — removing one of the junction links would break other tooling that depends on the standard C:\Users\Tony\.claude location.

[ReqRes-sudo]

I believe this shares the same root cause. In my environment, accessing files through a Windows junction causes a repeated "outside working directory" warning on every tool call, with no way to suppress it via settings.json permissions.

Environment:

• Windows 11, Claude Code
• ~/.claude is a junction (mklink /J) pointing to a dotfiles directory on another drive

Symptom:

• Every file access through the junction triggers "Allow access to file outside working directory?" prompt
• Adding both the junction path and real path to settings.json permissions does not resolve it

Related: #34252 (my original issue, about to be auto-closed as duplicate)