wmfix

#!/usr/bin/python
#You may have to change some of these values to match display/dock/menubar sizes
xscr=1920
yscr=1080
yd=5
xd=80
xstart=0
ystart=44

xmax=xscr-xd
ymax=yscr-yd
import subprocess,os
output = subprocess.Popen(["wmctrl", "-l","-G"], stdout=subprocess.PIPE).communicate()[0].split("\n")
class win():
    def __init__(self, wid, desktop, x, y, w, h, name):
        self.wid = wid
        self.desktop = int(desktop)
        self.x = int(x)
        self.y = int(y)
        self.w = int(w)
        self.h = int(h)
        self.name = name
    def __str__(self):
        return __repr__(self)
    def __repr__(self):
        return "%s (%s): (%d,%d) @ (%d,%d):%d"%(self.name,self.wid,self.w,self.h,self.x,self.y,self.desktop)
wins=[]
for i in output:
    f=filter(None,i.split(" "))
    if(len(f)<7):
        continue
    wins.append(win(f[0], f[1], f[2], f[3], f[4], f[5]," ".join(f[6:])))
for i in wins:
    if i.x<0 or i.x>xmax or i.y<0 or i.y>ymax:
        w=min(i.w,xmax-40)
        h=min(i.h,ymax)
        x=0
        y=0
    elif (i.x+i.w)>xscr or (i.y+i.h)>yscr:
        x=i.x-xstart
        y=i.y-ystart
        w=xscr-x-xstart
        h=yscr-y-ystart
    else:
        continue
    cmd="wmctrl -i -r %s -e 0,%d,%d,%d,%d"%(i.wid,x,y,w,h)
    os.system(cmd)

This runs wmctrl which you will need to install for it to work.