When organizing files across multiple drives, many developers create shortcuts to relocated folders only to discover Windows Explorer treats them as second-class citizens. These shortcuts:

• Appear mixed with files rather than with folders
• Don't show in the navigation pane tree view
• Break many file operations expecting real folders

Windows shortcut files (.lnk) are fundamentally different from actual directories. The Explorer GUI deliberately separates them for good reason - they behave differently in key scenarios:

// Example of broken behavior in batch scripts
FOR /D %%G IN ("C:\Projects\*") DO (
    REM This will skip your shortcut folders
    ECHO Processing %%G
)

NTFS junction points create virtual folders that redirect to target locations while appearing as real directories:

mklink /J "C:\Projects\Archive" "E:\Backup\ProjectArchive"

Key advantages:

• Appears in Explorer's folder tree
• Works with all folder operations
• Persists even if target is unavailable

For bulk operations, use this PowerShell script to convert existing shortcuts:

$shortcuts = Get-ChildItem "C:\Links" -Filter *.lnk | 
    Where-Object { $_.Target -match '^[A-Z]:\\' }

foreach ($sc in $shortcuts) {
    $target = (New-Object -ComObject WScript.Shell).CreateShortcut($sc.FullName).TargetPath
    if (Test-Path $target -PathType Container) {
        Remove-Item $sc.FullName
        cmd /c mklink /J $sc.FullName.Replace('.lnk','') $target
    }
}

While junction points solve most issues, be aware:

• Require NTFS formatted drives
• Don't work across network boundaries (use symlinks instead)
• Can create circular references

For advanced scenarios, consider these alternatives:

# Directory symbolic link (works across networks)
mklink /D "C:\RemoteProjects" "\\Server\Projects"

# Hard link to directory (Windows 10+ only)
fsutil hardlink create "C:\Mirror" "D:\Original"

---

When working with large projects where source code needs to be organized across multiple drives, many developers create folder shortcuts (.lnk files) pointing to external storage locations. However, Windows Explorer doesn't treat these shortcuts as first-class folder objects in two crucial ways:

• They appear mixed with files rather than grouped with folders
• They don't appear in the navigation tree view on the left panel

1. Using Directory Junctions (mklink)

For local drives formatted with NTFS, create a directory junction instead of a shortcut:

mklink /J "C:\Projects\ExternalCode" "E:\Backup\SourceCode"

This creates a virtual folder that appears identical to a real folder in Explorer, with these advantages:

• Appears in tree view
• Maintains folder grouping
• Works with all file operations

2. Symbolic Links for Advanced Scenarios

For cross-drive solutions (even across networks), use symbolic links:

mklink /D "C:\Projects\RemoteAssets" "\\server\share\assets"

For those who must use traditional shortcuts, this registry tweak changes their appearance:

Windows Registry Editor Version 5.00

[HKEY_CLASSES_ROOT\lnkfile\ShellEx]
"FolderClass"="{0AFACED1-E828-11D1-9187-B532F1E9575D}"

Warning: This only affects visual grouping, not tree view behavior.

For batch processing multiple folders, use this PowerShell script:

$source = "D:\Development\Libraries"
$dest = "C:\Dev\ExternalLibs"

Get-ChildItem $source -Directory | ForEach-Object {
    $linkPath = Join-Path $dest $_.Name
    New-Item -ItemType Junction -Path $linkPath -Value $_.FullName
}

Tools like Link Shell Extension provide GUI management for hard links, junctions, and symbolic links with right-click context menu integration.