Hi
In the last few days I learned to make a FTP to a device with Filezilla and / or CMD and use CMD on files 
I have back-up all files in my E4, CMD can read the E4 files, and Python is also recognized by Windows, so far so good.
In the step by step instruction (see image) I read;
"If all that works, type "quit" to exit and close ftp connection"
and a few lines further:
"it will read two files from your cam and stores them in a backup folder"
Question: how can Python read files from the camera if the ftp connection is closed?
And also:
" you will find newly created conf.cfc and common_dll.dll in that folder and upload them back to the camera"
"In case you get an error 500 at the upload, you have to upload the files manually by FTP"
thus in both cases I must manually upload the files?
Garrett
If all your files are in the same folder all you have to do is open cmd, switch directories to that folder (ex. "cd C:/Python27"), then in cmd write
"python apply.py apply 192.168.0.2"
first word is python for the app
second is to run the apply.py "program"
apply is to tell it to run the apply command
192.168.0.2 is the ip of your cam(you can check this by typing ipconfig into cmd) sometimes it is 192.168.1.2 for people or something similar
after that it should automatically upload the files to the camera, if it fails go into FileZilla and upload them manually(i've never seen anyone have to do this)
Then take the .cfc file in the camera(MAKE SURE YOU "REFRESH" THE DIRECTORY IN FILEZILLA TO UPDATE TO THE NEW CFC FILE) and drop it in the python27 folder where all your files are and click/run the menu_conf.py, then take the new conf.cfc file it created and upload it to the camera. after this you just go into flirinstallnet and run the 2.3.0 menu.fif file and wa la you have a fully modified cam.