This script using arcpy to consolidate all the feature layers in a map document into a single File GDB

consolidate_layers.py

import arcpy
import time
import os

mxd = arcpy.mapping.MapDocument(r'C:\<path>\<to>\<map>.mxd')
dfs = arcpy.mapping.ListDataFrames(mxd)

file_gdb = r'C:\<path>\<to>\<file>.gdb'


def copy_features(in_layer):	
	try:
		if arcpy.Exists(os.path.join(file_gdb, layer.datasetName)):
			print 'Already exists, renaming'
			new_name = in_layer.datasetName + str(time.time())
		else:
			new_name = layer.datasetName
		
		arcpy.CopyFeatures_management(layer, os.path.join(file_gdb, new_name))	
	except:
		print 'Error copying', layer.name

		
for df in dfs:
	print 'Dataframe:', df.name
	layers = arcpy.mapping.ListLayers(mxd, '', df)	
	for layer in layers:
		if layer.isFeatureLayer:
			print 'Copying:', layer.name
			copy_features(layer)