Since I found out that NTFS now has semi-working native symlinks, I have updated the symlinking script used in the Combining an Android Project's Versions post. This script creates relative symlinks now through Perl instead of absolute hard links through Bash. It is as follows:

#!/usr/bin/perl
#Run this file to install links to shared files into all branches
use warnings;
use strict;

#Configuration
my $SharedDirectoryName="Shared";
my $NonProjectDirectories="^\\.(|/\\.git|/$SharedDirectoryName)\$"; #Non Project directories (., .git, $SharedDirectoryName)
my $IsWindows=(index(lc(`uname`), 'cygwin')!=-1);

#Create a symlink
sub MakeLink
{
	my ($LinkTarget, $LinkName, $IsWindows, $IsDirectory)=@_;

	#Create the target directory if it does not exist
	my $LinkDirectory=$LinkName;
	$LinkDirectory =~ s/\/[^\/]+$//;
	if(!-e $LinkDirectory) {
		print "Creating directory: $LinkDirectory\n";
		`mkdir -p "$LinkDirectory"`;
	}
	
	#If the link already exists, issue a warning
	if(-l $LinkName) {
		print "Link already exists: $LinkName\n";
		return;
	}

	#Create the relative symlink
	my $RelativePathFromLinkToTarget=('../' x ($LinkName =~ tr/\///)).$LinkTarget; #Determine the relative path between the link and its target
	my $Command;
	if(!$IsWindows) { #Create the Linux command
		$Command="ln -s \"$RelativePathFromLinkToTarget\" \"$LinkName\"";
	}
	else #Create the Windows command
	{
		#Replace /s in path with \s
		$RelativePathFromLinkToTarget =~ s/\//\\/g;
		$LinkName =~ s/\//\\/g;
		
		$Command='cmd /c mklink'.($IsDirectory ? ' /d' : '')." \"$LinkName\" \"$RelativePathFromLinkToTarget\"";
	}

	print "$Command\n";
	`$Command`;
}

#Find required information from file searches
my @LocalBranches=grep(!/$NonProjectDirectories/, `find -maxdepth 1 -type d`); #Find version folders by ignoring Non Project directories
my @Files=split(/\n?^$SharedDirectoryName\//m, substr(`find $SharedDirectoryName -type f`, 0, -1)); shift @Files; #Find shared files

#Propagate shared files into different versions
foreach my $LocalBranch (@LocalBranches) {
	$LocalBranch=substr($LocalBranch, 2, -1); #Remove ./ and new line separator
	foreach my $File (@Files) {
		MakeLink("$SharedDirectoryName/$File", "$LocalBranch/$File", $IsWindows, 0);
	}
}