Here is a quick guide I made for bundling PS4 game updates into PKGs. PKG Kitchen 1.3 is used and all thanks to the toolmakers...
Game Update PKG
Needed: PKG Kitchen 1.3, Offline Update PKG ≤4.05
1: Insert game disc and install
2: Exploit idc, xvortex ftp payload
3: Dump 4 files from system_data/priv/appmeta/CUSAxxxxx/* to dump\appmeta\ (Must get these files before update)
4: Exit title/ftp, reboot, exploit xvortex, install sony game update pkg (This will be the hardest step, obtaining offline 4.05 updates)
5: Check for update to game on information screen
6: Reboot, exploit idc, xvortex ftp payload, minimize, load game, connect ftp
7: Dump /user/app/CUSAxxxxx/app.pkg -> dump\pkg
/mnt/sandbox/pfsmnt/CUSAxxxxx-app0-nest/pfs_image.dat -> dump\pfs\
/mnt/sandbox/pfsmnt/CUSAxxxxx-app0/sce_module/* -> dump\app\sce_module\
/mnt/sandbox/pfsmnt/CUSAxxxxx-patch0-nest/pfs_image.dat, RENAME pfs_image2.dat -> dump\pfs\
/mnt/sandbox/pfsmnt/CUSAxxxxx-patch0/eboot.bin -> dump\app\
/mnt/sandbox/pfsmnt/CUSAxxxxx-patch0/sce_module/* -> dump\app\sce_module\ (Overwrite if prompted, update may not contain this folder and/or all files)
8: Reboot, remove disc, and delete game and all game data
9: Run _extract_pkg.bat and wait for success
10: Open /tools ArchiveExplorer.exe and open dump\pfs\pfs_image.dat and extract all to \app\
11: Open dump\pfs\pfs_image2.dat and extract all and overwrite to \app\
12: Copy and overwrite dump\app\* to \app\
13: Copy and overwrite dump\appmeta\* to \app\sce_sys\
14: Run _gen_gp4.bat and wait for success
15: Open CUSAxxxxx.gp4 with /tools/orbis-pub-gen.exe and go to Command, Build Image, select save location and build.
16: Turn on PS4, load xvortex exploit, install new PKG with bundled update.
How to Install Older PS4 Game Updates on Any PS4 7.02/7.50
Installing PS4 Games, DLC & Updates (PS4 6.72 Jailbreak)
Installing Retail Updates on a Jailbroken PS4 (6.72 or Lower!)
Backing up Retail Games to Fake Pkg's (6.72 or Lower)
Game Update PKG
Needed: PKG Kitchen 1.3, Offline Update PKG ≤4.05
1: Insert game disc and install
2: Exploit idc, xvortex ftp payload
3: Dump 4 files from system_data/priv/appmeta/CUSAxxxxx/* to dump\appmeta\ (Must get these files before update)
4: Exit title/ftp, reboot, exploit xvortex, install sony game update pkg (This will be the hardest step, obtaining offline 4.05 updates)
5: Check for update to game on information screen
6: Reboot, exploit idc, xvortex ftp payload, minimize, load game, connect ftp
7: Dump /user/app/CUSAxxxxx/app.pkg -> dump\pkg
/mnt/sandbox/pfsmnt/CUSAxxxxx-app0-nest/pfs_image.dat -> dump\pfs\
/mnt/sandbox/pfsmnt/CUSAxxxxx-app0/sce_module/* -> dump\app\sce_module\
/mnt/sandbox/pfsmnt/CUSAxxxxx-patch0-nest/pfs_image.dat, RENAME pfs_image2.dat -> dump\pfs\
/mnt/sandbox/pfsmnt/CUSAxxxxx-patch0/eboot.bin -> dump\app\
/mnt/sandbox/pfsmnt/CUSAxxxxx-patch0/sce_module/* -> dump\app\sce_module\ (Overwrite if prompted, update may not contain this folder and/or all files)
8: Reboot, remove disc, and delete game and all game data
9: Run _extract_pkg.bat and wait for success
10: Open /tools ArchiveExplorer.exe and open dump\pfs\pfs_image.dat and extract all to \app\
11: Open dump\pfs\pfs_image2.dat and extract all and overwrite to \app\
12: Copy and overwrite dump\app\* to \app\
13: Copy and overwrite dump\appmeta\* to \app\sce_sys\
14: Run _gen_gp4.bat and wait for success
15: Open CUSAxxxxx.gp4 with /tools/orbis-pub-gen.exe and go to Command, Build Image, select save location and build.
16: Turn on PS4, load xvortex exploit, install new PKG with bundled update.
How to Install Older PS4 Game Updates on Any PS4 7.02/7.50
Installing PS4 Games, DLC & Updates (PS4 6.72 Jailbreak)
Installing Retail Updates on a Jailbroken PS4 (6.72 or Lower!)
Backing up Retail Games to Fake Pkg's (6.72 or Lower)