#!/usr/bin/python

import os
import sys
import shutil

if len( sys.argv ) < 3:
	sys.stderr.write( 'Usage: ' + sys.argv[0] + ' [inputDir] [outputDir]\n' )
else:
	rootPath = sys.argv[1];
	outDir = sys.argv[2];

	headers = []
	sources = []
	unknown = []

	for root, dirs, files in os.walk( rootPath ):
		for filename in files:
			if filename.endswith( '.h' ):
				headers.append( [ root, filename ] )
			elif filename.endswith( '.cpp' ) or filename.endswith( '.c' ):
				sources.append( [ root, filename ] )
			else:
				unknown.append( [ root, filename ] )

	def getTargetPath( root, folder, filename ):
		newRoot = root.replace( rootPath, '' )
		if newRoot.startswith( '/' ):
			newRoot = newRoot[1:]
		targetDir = os.path.join( outDir, folder, newRoot )
		if not os.path.exists( targetDir ):
			os.makedirs( targetDir )

		return os.path.join( targetDir, filename )

	for file in headers:
		fromPath = os.path.join( file[0], file[1] )
		toPath = getTargetPath( file[0], 'include', file[1] )
		shutil.copyfile( fromPath, toPath )

	for file in sources:
		fromPath = os.path.join( file[0], file[1] )
		toPath = getTargetPath( file[0], 'src', file[1] )
		shutil.copyfile( fromPath, toPath )

	for file in unknown:
		fromPath = os.path.join( file[0], file[1] )
		toPath = getTargetPath( file[0], 'unknown', file[1] )
		shutil.copyfile( fromPath, toPath )		

The results would be something like this:

Input:
/aardvark.h
/stuff.h
/stuff.cpp
/main.cpp
/widgets/doodad.h
/widgets/doodad.cpp

Output:
/include/aardvark.h
/include/stuff.h
/include/widgets/doodad.h
/src/stuff.cpp
/src/main.cpp
/src/widgets/doodad.cpp

Another fun perk of working from home.