nevermind crushev I was being a fool. Your tool works perfecto. What was happening is on my pc at least it takes a long time to extract and post the green wording success screen. I waited a little longer after the extraction gave the finish message and poof it appeared:
Glad you got it worked out
And thanks for the credit in the video. The success you see at first (before green screen) is actually a success for part of the process (those are debug messages during decompression). It actually keeps doing stuff until the green Success screen. When you say that you have had the tool not take care of some stuff for you thats probably because you tried doing stuff before the green success screen, it takes care of all those folders for you at the very end of the whole process. So if you didnt wait long enough then yeah those files will still be there. If you try to do anything before green Success screen its like for example unpacking a rar or zip with 100 files inside, and trying to do stuff only after the first couple are unpacked. You will be missing stuff.
The estimated time that is given is calculated based on pkg file size. It will differ a bit from PC to PC and .pkg file to .pkg file. In your video you are using 3Gb update file, but it actually unpacks to 5Gb file. meaning things are packed pretty tightly and not surprising it takes longer. So better estimate for that particular file would have been based on 5GB size. Problem is that I cant tell how big its going to be before unpacking, so the packed size is the best guess I can make. Most pkgs from my experience arent compressed very much so from my experience estimate tends to be pretty accurate. Although it will also depend on your CPU speed and if you are on an SSD or not.
EDIT - looking at the video again, it looks like you are doing this on an external USB drive. This will basically halve (or more) your speed and will definitely be slower if you are using USB2.0. Because essentially the file is read to your C drive by Windows, then extracted to temp file, then copied back to the USB drive. This is how any extraction would work on USB drive (like if you unzip something from a USB drive same thing happens, Windows copies the file to its working directory, extracts it to temp then copies back to USB drive). The part that really slows things down is that it does it sequentially so its reading and writing from/to USB drive at the same time, which really kills the USB's throughput. You are probably getting close to 10mb/sec there. and with 3GB pkg and 5 GB final file you are essentially transferring 8Gb over USB. Which would take around 13 to 15 minutes. As opposed to doing it on a SATA drive (internal drive), you arent copying the initial 3GB, Windows would extract to temp, then move the files to final directory (moving is essentially free), so you would only copy about 5GB, but on SATA you would get at least 50Mb/sec throughput (probably more, especially if SSD), which would take about a minute to 2 minutes for the 5GB folder, the program gives estimate based on initial pkg size which is 3GB, so for 3GB it would take (3 * 1024 / 50 / 60) = 1.1 minute.
Now in your situation its probably fine to just wait, because if you are first going to copy the file to internal drive to do this then copy resulting pkg back you probably wont save much time. Basically the lesson here is that if you are doing this on a USB drive expect much slower speeds (10 to 15 times slower than what the program estimates). So if it says 1 minute, expect 10 to 15..
The tool uses standard Windows libraries, so it should never hang for no reason, it will either succeed or give you an error. So if you dont have an error then just wait (you can check folder size to see if its increasing, and/or most USB drives have an activity LED, see if its blinking).
For installing on the PS4, you dont need to remove the game, just install right on top. And to tell if it worked or not on the dashboard press the Start button (or whatever its called these days) when the game is highlighted and go to "infromation" it will tell you version # there.
Also, if you type in the first letter or first few letters of the pkg name then hit tab it will go straight to it, so you dont have to TAB cycle through all the different files before you get to it.