PowerShell script to make ~\Documents more usable, hides directories and makes them accessible via a symlink in a different location.

Manage-AppConfig.ps1

param(
    [Parameter(Position=0)]
    $Item,
    [Switch] $WhatIf,
    [String] $AppConfig = "$env:HOMEDRIVE$env:HOMEPATH\AppConfig",
    [String] $BaseDir = ".",
    
    [Parameter(ParameterSetName="register")]
    [Switch]
    $Register,
    
    [Parameter(ParameterSetName="unregister")]
    [Switch]
    $Unregister);

# Clean up your ~, and ~\Documents directories on Windows while not breaking any of the applications that use it
# Usage: .\Manage-AppConfig.ps1 -Register Documents\SomeStupidApp
# Will 
#  - create a symlink to Documents\SomeStupidApp in ~\AppConfig\Documents\SomeStupidApp
#  - hide Documents\SomeStupidApp
#
# You can configure ~\AppConfig to be something different, I wouldn't necessarily use ~\AppData, though because I have seen programs that use BOTH locations :-(
# By default the path under ~\AppConfig is the same as the path you specified (MUST be relative), but you can also explicitly specify the BasePath.
#
# Provided AS IS. It might not work. It might break something and destroy 5 years of your hard work in 5 seconds, or less.

$ErrorActionPreference = "stop";

Write-Debug "Item: $Item";
Write-Debug "BaseDir: $BaseDir";
Write-Debug "AppConfig: $AppConfig";

$WhatIfPreference = $WhatIf;

function Get-Attributes($Path){
    (Get-Item -Path $Path).Attributes
}

function Hide-File($Path){
    $i = Get-Item $Path -Force;
    if(-not ($i.Attributes -match "Hidden")){
        $i.Attributes = @("Hidden") + $i.Attributes;
    }
}

function Unhide-File($Path){
    $i = Get-Item $Path -Force;
    Write-Debug "unhiding: $($i.Attributes)";
    if($i.Attributes -match "Hidden"){ 
        $n = [IO.FileAttributes]($i.Attributes -bxor [IO.FileAttributes]::Hidden)
        Write-Debug "newattributes: $n"
        $i.Attributes = $n;
    }
}

if(-not (Test-Path $AppConfig)){
    Write-Debug "AppConfig at $AppConfig does not exist. Creating it now."
    New-Item $AppConfig -ItemType "directory";
}

function Check-Status($Path){
    $AbsolutePath = [System.IO.Path]::GetFullPath((Join-Path $BaseDir $Path));
    if(-not (Test-Path $AbsolutePath)){
        Write-Debug "Cannot find item to manage: $AbsolutePath"
        throw "Cannot find item to manage: $AbsolutePath";
    }
    $Item = Get-Item $Path -Force; # -Force because hidden items will not be found otherwise
    $MirrorPath = [System.IO.Path]::GetFullPath((Join-Path $AppConfig $Path));
    
    if(Test-Path $MirrorPath){
        Write-Debug "Mirror $MirrorPath exists";
        $mirror = Get-Item $MirrorPath;
        if([bool]((Get-Attributes $MirrorPath) -band [System.IO.FileAttributes]::ReparsePoint)){
            Write-Debug "Mirror $MirrorPath is a reparse point";
            if($mirror.ReparsePoint.Target -eq $Item.FullName){
                Write-Debug "Mirror $MirrorPath already points to $Item.";
                $status = "exists";
            } else {
                Write-Debug "Mirror $MirrorPath points to different item $($mirror.ReparsePoint.Target)";
                $status = "conflicting";
            } 
        } else {
            Write-Debug "Found ordinary file/directory in mirror at $mirror.";
            $status = "invalid";
        }
    } else {
        Write-Debug "Mirror $MirrorPath does not exist (yet)."
        $status = "none";
    }
}

$visibilityAction = "none";

switch($PsCmdlet.ParameterSetName){
    "register" {
        Write-Debug "Register $Item into AppConfig at $AppConfig.";
        . Check-Status $Item
        switch ($status){
            "exists" {
                Write-Verbose "Correct mirror already exists at $MirrorPath.";
                $visibilityAction = "hide";
                break;
            }
            "invalid" {
                Write-Error "Ther mirror's location is occupied by a different item: $mirror (not a reparse-point)";
                break;
            }
            "conflicting" {
                Write-Error "There is already a mirror in place pointing at a different location: $($mirror.ReparsePoint.Target)";
                break;
            }
            "none" {
                Write-Verbose "Installing mirror from $MirrorPath to $Item.";
                $fp = [System.IO.Path]::GetFullPath($MirrorPath);
                if($WhatIf){                    
                    Write-Host "Creating symlink from $fp to $Item.";
                } else {
                    Write-Debug "fp=$fp";
                    New-Item -ItemType "directory" -Force ([IO.Path]::GetDirectoryName($fp))
                    New-Symlink "$fp" -TargetPath "$Item";
                }
                $visibilityAction = "hide";
                break;
            }
            default {
                Write-Error "Unknown state.";
                break;
            }
        }
        break;
        
    }
    "unregister" {
        Write-Debug "Unregister $Item from AppConfig at $AppConfig.";
        . Check-Status $Item
        switch ($status){
            "exists" {
                Write-Verbose "Expected mirror found at at $MirrorPath. Removing it.";
                if($Whatif){
                    Write-Host "Removing reparse point at $MirrorPath.";
                } else {
                    Remove-ReparsePoint "$MirrorPath";
                }
                $visibilityAction = "show";
                break;
            }
            "invalid" {
                Write-Error "Ther mirror's location is occupied by a different item: $mirror";
                break;
            }
            "conflicting" {
                Write-Error "The mirror points at a different location than expected: $($mirror.ReparsePoint.Target)";
                break;
            }
            "none" {
                Write-Verbose "No mirror found at $MirrorPath.";
                $visibilityAction = "show";
                break;
            }
            default {
                Write-Error "Unknown state.";
                break;
            }
        }
        break;
        
    }
}

switch($visibilityAction){
    "show" {
        Write-Verbose "Un-hiding $Item";
        Unhide-File $Item;
        break;
    }
    "hide" {
        Write-Verbose "Hiding $Item";
        Hide-File $Item;
        break;
    }
}