Backup ALL Android files to PC? I've had this issue with both my GS3 and now my N5. I routinely wipe my phone and start over fresh, so using apps like TitaniumBackup and Helium does not help me since I don't plan on restoring any of my apps in the future. 

My problem arises when I connect my phone to either my PC or my Mac laptop, and attempt to just backup ALL of the files ("Backup ALL the files!") to my computer or an external hard drive. The computer will start copying the files, but then the progress bar disappears after a few seconds (well before hitting 100%) with no errors or messages. Upon checking the copied files, some folders and files are completely backed up with a simple drag and drop, but other folders don't. 

I have the phone set on MTP and debugging is enabled, and all of the files show up. I realize that some folders don't allow you to just drag and drop them (possibly the "Android" folder?), but others, like my "Downloads" folder, shouldn't have any restrictions, right? 

How can I simply make a full backup of all of the files that are on the phone? I've done this successfully in the past, but cannot remember what method or program was used.
MTP might not be reliable enough for that. Several approaches I can offer:

using on-board capabilities via ADB

This requires ADB tools being available on your computer (see e.g. Is there a minimal installation of ADB? for how to meet this). Now let's see how to get the files over.


open a command prompt, and (optionally) switch to the directory your adb executable is in
Make sure usb-debugging is activated on your device
connect your device via USB
assuming your SDCard is mounted/available as /sdcard on your device, let's copy it with its contents:

adb pull /sdcard /home/chris/android/sdcard



Just adjust the path to your needs ;)

using an app with a more user-friendly GUI

I use FolderSync to keep several directories backed-up. The big pro of this approach is: even if your device hard-crashes one day, you still have a quite up-to-date backup of all files on your computer.

 
FolderSync: Main screen, folder pairs (source: Google Play; click images for larger variants)

FolderSync supports a lot of services and protocols – not only cloud storage. You can easily use it with Windows shares (aka Samba aka SMB), or via SCP on Linux, or FTP with any server, amongst others. Simply define folder pairs (which directory on your device shall be kept in sync with which remote directory), and setup a schedule (e.g. whenever connected to your home WiFi, at 3 am), and there you go. With the Pro version (which I use) you can even set it to "manual only", and trigger it via tasker.

Of course, you also can set it to "manual", and then initiate the transfer whenever you find it useful. Being a "Sync tool", it will always only copy those files needing to be copied – if the same file exists on both ends with the same content and timestamp, it doesn't need to be copied again ;)

Other options

Plenty of them. More sync tools. Or a remote manager like AirDroid. Or using a file manager with remote capabilities, like ES File Explorer. Just to give you some ideas ;)