[Q] Integrating updates of system apps (and/or downloaded apps) into ROM - Kyocera Zio M6000

Okay. I don't have a lot of knowledge on developing/tinkering on Android, but I think I've figured out how to integrate apps into the ROM (updates of system apps and/or downloaded apps). I used:
A stock cricKet 2.2.1 ROM, rooted (of course) w/Universal Androot
Root Explorer, and
ROM Manager (more on this later)
First thing is first, I did a TI backup; don't want to lose anything
I then opened Root Explorer
Mounted R/W, and
did a search for .apk.
Notice that the only directories the actual .apk files for INSTALLED apps should appear in (outside the SD card) are:
/cache
/data/app
/data/app-private (possibly)
/data/FLEX/app
/system/app
Ignore the following:
/cache
/data/FLEX/app
Now, you may already know this, but the system apps you're looking for are located in the /system/app directory, and downloaded apps (for the updated system apps) are located the /data/app directories that aren't being currently ignored (if you're following my instructions). Based on icon, filename, and common sense, I found which .apk files were the updates of already existing system apps (IE Market, Google Maps, Voice Search, etc.) in the /data/app directory, and the corresponding system app they updated in the /system/app directory. I then:
Copied the filename of the system app I was going to replace (rename copy all)
Moved over to the /data/app directory
Located the corresponding updated app
Renamed it what its corresponding system app was renamed (rename, delete existing name, paste)
Hit the 'move' option
Navigated to the /system/app directory
Deleted original system app (you may want to backup this file beforehand)
Pasted the updated system app
Within 30 seconds or so, you should get a (blah.blah.blah has unexpectedly shut down force close/report) popup. Just hit force close and you should be fine (Google Maps seemed to be a recurring FC). If you try to open the app before rebooting, it will force close on you. When you're finished, open ROM Manager. I know you're thinking 'This app is no good on the ZIO'; so stop. Hit 'Fix Permissions'. The reason for this is that it fixes a few rare force close issues. I don't know the mechanics of it, but it works, so I don't question it. Listen to the notification you'll see and reboot your phone after it finishes fixing the permissions. Now go into settings and manage applications, and you'll see that you can no longer uninstall whatever apps you moved to the /system/app directory.
FYI Renaming .apk files doesn't seem to make a bit of difference either way.
(Forgive my horrible perspective descriptions: I/you)
I haven't tested it yet, but I believe unrooting the device should make any apps moved to the /system/app directory that require root access would become non-functional (right?). The reason this thread is a question is that I'm wondering if i did this correctly, and if so, I want to find out if unrooting and factory resetting my phone would somehow delete the apps in the /system/app directory that weren't included in the stock ROM. (I'm not really willing to do that yet; I still have to download the SDK to my new computer so I can do a NANDROID backup.) Any help answering these from a more experienced developer would be great.

If you want to incorporate apps into a rom, the apps have to be free or you must get consent from the developer to include in your rom
Sent from my Zio using XDA Premium App

Only if it is a Public rom. Even free app developers should be credited in a public rom

Mattix724 said:
If you want to incorporate apps into a rom, the apps have to be free or you must get consent from the developer to include in your rom
Sent from my Zio using XDA Premium App
Click to expand...
Click to collapse
I'm operating under the assumption that you're using Google developed updates of system apps. I suppose I should have said something to that extent up top.
[UPDATE]
Okay, so I did a NAND and then factory reset my phone. Killed everything not in the /system/app directory. I'm sure you knew that would happen, but I guess I'm posting for the noobs. Easier to find, I guess.

Hi,
I've tried to integrate some apps using Titanium Backup but it stuch at 0% for more than 5mins so I cancelled the process. Is it normal that it was that slow? Does Titanium generate odex files too?
I've tried integrating updates for GoogleMaps, StreetView and Youtube using a recovery mode and ADB on my linux machine.
After the backup system data I've deleted original apk and odex files from /system/app/ and moved newer versions from /data/app/ to /system/app/.
I renamed the files from com.google.android.blah.blah.apk to old names (ie. Maps.apk, etc). I haven't generated the odex files.
Rebooted the phone (HTC Desire, 2.2, Orange UK) and these apps were not available. I couldn't run either GoogleMaps or Youtube. They weren't on the "All apps" list, but still were in the system app manager/uninstaller, but couldn't uninstall them as they were in system obviously.
Tried to clear Dalvik cache but no difference.
Then I've copied them with my user backed apk files (it went to /data/app and installed the newest versions) and all is fine - could launch them as usual.
Now using "adb push" method I copied my old system versions of these apps in the /system/app/ and all if fine. I could updated them to newer versions, but this obviously went to /data/app/, so didn't free the phone memory.
Any idea why integrated apps were not visible in the system?
Perhaps I shall just delete the old system apps and copy the ones from /data/app/ without renaming...
Much appreciate it.
Greg
edit:
All went fine now. Just deleted old files in the /system/app and moved newer version without renaming to from /data/app

use titanium backup and choose integrate updates into rom for the app

I don't want to pay for TB premium. I'm poor.
Sent from my Zio using XDA App

TB integrating not working on some phone (including mine) anyway.

Related

[Question] How to pull .apk's to use with different ROMs

I've been switching back and forth in recovery between Modaco's desire rom and CM. Recently I downloaded a couple beta's on the desire rom, which are all now closed, that I'm trying to get back on my CM rom. Is there a way to pull the .apk out of the Desire rom so I can use it with my CM? (Or with froyo or the new desire builds when they come out).
Thanks
Use Titanium Backup. Available for free in the market
Or you could use adb and pull the apks for /system/app or /data/app depending on where it was installed... even if you have app2sd, pull from /data/app will work since it is symlinked...
Code:
adb pull /system/app .
adb pull /data/app .
Most desire apks are not compatible with CM or any other non-sense ui roms.
Search a little and you'll know what i mean
PhantomRampage said:
Most desire apks are not compatible with CM or any other non-sense ui roms.
Search a little and you'll know what i mean
Click to expand...
Click to collapse
If you read the first post, OP wasn't talking about desire app apk, but rather some 3rd party beta apps apks...
Slighty OT.
When I download & install an app from the market, where does its apk get stored on my Nexus running OS2.1? I went looking but could only find the inbuilt apps in the /system/app folder. I have a couple of apps that I would like to copy to my SD card with ASTRO prior for backup purposes. Thanks.
logger said:
Slighty OT.
When I download & install an app from the market, where does its apk get stored on my Nexus running OS2.1? I went looking but could only find the inbuilt apps in the /system/app folder. I have a couple of apps that I would like to copy to my SD card with ASTRO prior for backup purposes. Thanks.
Click to expand...
Click to collapse
Depending on the install type specified... the app would either install as a normatl app or a protected app...
Normal apps are stored in /data/app, protected in /data/app-private
craigacgomez said:
Depending on the install type specified... the app would either install as a normatl app or a protected app...
Normal apps are stored in /data/app, protected in /data/app-private
Click to expand...
Click to collapse
The thing is, my /data folder appears as empty and I have 80 apps installed!! I am using ASTRO file manager.
Winzip/winrar
logger said:
The thing is, my /data folder appears as empty and I have 80 apps installed!! I am using ASTRO file manager.
Click to expand...
Click to collapse
Maybe astro can't view the list of files there... I can't list the files there in the terminal application without getting su privileges... use adb pull to get the files...

[HowTo] Remove preinstalled apps - no need to flash custom roms or gold card root!

I know there are some people like myself who actually like Sense and doing a 'full' root can be daunting, especailly if all you want to do is remove the crud that Vodafone or your Telco install on your branded Legend. But there is no reason this can't be used to remove apps that are in a custom ROM - as far as I am aware! If someone with a custom ROM could confirm this, that would be great!
Righto, as per usual here is the disclaimer - doing this is risky and you do so at your own peril! Don't come crying to me or Paul @ MoDaCo if it bricks your phone (it shouldn't but this is just a warning)
Enough of that you get the idea Now for the fun bit!
First if you are not you'll need VISIONary+ from MoDaCo, at the time of this writing r13 is the latest and is available on page 7.
Please read and check the original post as there may be an updated version. If you are rooted skip to the next step.
This is Paul's guide he done quickly on his G2, it's more of a pictorial guide (same rules apply to the Legend as G2 in this case).
Once installed use the Temproot option, this can take 15 seconds or so to complete, use a Terminal Emulator and type su then return/enter and your $ should change to a # - this means you have temproot.
Go to the market and install SuperUser, Titanium Backup, BusyBox.
Open Titanium Backup allowing it root access when prompted, go to Backup/Restore and scroll to find one of the preinstalled bloatware apps, I chose the Vodafone Music app and the Vodafone Web app.
Long hold on the app you want to remove and scroll down a bit and choose the option "Force remove app (by recovery exploit)"
This will reboot your phone TWICE, you will get the recovery screen up - LET IT RUN IT's COURSE! DO NOT INTERRUPT THIS.
Once it boots back into your normal check that the app is no longer in your App drawer
Repeat for all the Apps that came preinstalled that you don't want, just be careful you don't remove anything that may still be needed!
A huge thanks to Paul at MoDaCo for this ingenious hack and the Titanium Backup, BusyBox and SuperUser developers for their hard work in writing their apps which also allow us to easy do this
Oh and you can use the Temproot on boot to have a sortof but not fully permaroot
Great work. I'll try on CM 6.1 RC1. One thing though...If I'm rooted I presume I need only the Titanium backup not VISIONary or other tools, right?
Yes you need the other apps, but you can remove them afterwards if you want. You'll need SuperUser to be able to grant Titanium Backup access, and Titanium Backup requires BusyBox to be installed - Titanium Backup gives you the option to install BusyBox if you press the 'Problems?' button under the Overview tab.
PS: you can use the free version of Titanium Backup for this exercise.
Yes, thank you. I knew about busybox and the option to install it from Titanium. SuperUser I have it already since I'm using CyanogenMod RC1 and it is included in the ROM (I think it is OK like this). So only Titanium (+busybox) needs to be installed.
I'll give it a try and let you know the results. I'll try to remove a rather large application (for ex Google Maps) and I'll install it afterward on the sdcard (since it is system appl, it cannot be moved directly to sdcard)
Later edit: IT WORKS! So I've tried to (and succeeded) remove 2 "system" applications: Google Maps and Calculator. Both were removed and the free space is now available (before 80 Mb free, after 91.2 Mb free).
There was only one issue with Maps, the icon still showed up in the application drawer and it was working (even after going through all above). After several checks I found the reason. The Maps were installed twice...the version included in the CM ROM (that was deleted by this procedure) AND the updated Maps (it once asked for upgrading the application from the market and I did that). After removing the "system installed" version of Google Maps, the "updates" remained. I went to Settings-Applications-Manage Applications and I found Maps there. I've uninstalled the updates then rebooted the phone. After that the icon was gone completely.
To conclude, for CM ROMS (or for all phones that are already rooted and have already the SU application), the steps to be performed for removing a system appl are:
1. Install Titanium Backup
2. Press (as instructed) "Problems" button. This will install a working version of busybox.
3. Check if the application you want to remove, has also updates (from Market or some other places) installed. If YES, go to Settings-Applications-Manage Applications and uninstall all the updates.
4. Start Titanium Backup and perform the steps indicated in the first post by TheLegendaryJay.
So it is working on custom ROM's as well and you don't need VISIONary or other application/tools.
All credits go to Paul, CM team and this whole community, the ones which made such things possible for our phones. TheLegendaryJay, thank you also for sharing this with us. Perhaps for rooted phones it is easier to remove applications with adb commands, but some are maybe not so technical to install the SDK or know how to use it (I can be counted as one of them), or they just might want to remove an application when they don't have a pc with SDK nearby.
yap, can confirm this. works great on cm 6.1 rc1. thanks for the hint
For you guys who are rooted - why not just flash the overlay filesystem patch, enable it, and then use any file explorer and go to /system/app/ and delete the apps you dont want? just a tip, it's much easier.. (and takes less time)
Because one of the reasons for which I wanted to rip out an application from the ROM is to gain some more space... By using overlay system, as I understood, you're practically duplicate the whole system to make it accessible for writing so I don't know if you gain some more space. Eventually you'll have less. Or, if that space is on the sdcard, that does not suit me also cause as I know, is working slower from there. Anyhow, I don't want to detail this here cause we'll be off-topic.
Rapier said:
Because one of the reasons for which I wanted to rip out an application from the ROM is to gain some more space... By using overlay system, as I understood, you're practically duplicate the whole system to make it accessible for writing so I don't know if you gain some more space. Eventually you'll have less. Or, if that space is on the sdcard, that does not suit me also cause as I know, is working slower from there. Anyhow, I don't want to detail this here cause we'll be off-topic.
Click to expand...
Click to collapse
As I understand it, the system folder is only linked so the phone believes it's on the SD-card. This should mean, no extra space is taken (except for the few kB that makes this possible). i could be wrong, but I use system overlay and I see no whatsoever decrease in performance. Not in benchmarks nor in usage.
If you are rooted - and dont want system overlay, I still think there is a better wway - ADB! just mount system, cd to system/app, ls it and rm whatever apps ypu dont want.. no need for multiple reboots - quick and effective
adb way might be quicker but it might prove to be ineffective (at least for me it was). In order to remove an application, you must check its filename (with ls command). I've tried to remove Facebook and Twitter applications using adb remove and guess what...they're still there. I admit I might have done something wrong, what I'm saying is that through this new method described above, someone is able to remove an appl by chosing it from a list. For the ones that don't feel so confortable using adb, this is an alternative
Sent from my Legend using XDA App
Rapier said:
adb way might be quicker but it might prove to be ineffective (at least for me it was). In order to remove an application, you must check its filename (with ls command). I've tried to remove Facebook and Twitter applications using adb remove and guess what...they're still there. I admit I might have done something wrong, what I'm saying is that through this new method described above, someone is able to remove an appl by chosing it from a list. For the ones that don't feel so confortable using adb, this is an alternative
Sent from my Legend using XDA App
Click to expand...
Click to collapse
When it comes to ADB, you must write the filename exactly as it is, if you want to remove Facebook.apk you must rm Facebook.apk, not facebook.apk or just rm Facebook*
What I do, I ls all files, copy the filenames I want to remove into into a txt file. ex. "rm facebook.apk Torch.apk voiceDialer.apk AndroidTerm.apk" and so on. When I flash a new rom, i just copy that file string and remove em all with that one command ofc. I ls it after and check if there is anything new I want to remove, but I get rid of most of it in a few seconds. (good tip!)
I understood that. Now I've checked again and I know what happened...the same thing I said above. The appl was removed also with adb command but the updates of that appl were not. I've removed the updates from Settings and after that the whole appl was gone (Facebook in this case). So both metods work, everyone can choose what he likes more
Anyway this was much more to test if it's working on custom ROMs as was asked by TheLegendaryJay and less as of providing an alternate way for rooted owners.
Sent from my Legend using XDA App
You both are wrong. Overlay is just an overlay... it uses several file systems or parts of file systems (directories, files), merge them and show them to us as one new merged file system. The principle is such that if U have one read-only and one read-write file system merged together, all writes are then performed to that read-write one. If you'd like to delete one file from read-only portion, that action is noted on read-write portion and your system doesn't t see that file again through merged file system whereas it is in fact still there...
BlaY0 said:
You both are wrong. Overlay is just an overlay... it uses several file systems or parts of file systems (directories, files), merge them and show them to us as one new merged file system. The principle is such that if U have one read-only and one read-write file system merged together, all writes are then performed to that read-write one. If you'd like to delete one file from read-only portion, that action is noted on read-write portion and your system doesn't t see that file again through merged file system whereas it is in fact still there...
Click to expand...
Click to collapse
thanks for this, great info. Now I'm glad I use adb and not file overlay for removing files
Why's that? Overlay is really handy thing for testing... U can make the system think that the file is not there but in fact is. If something goes wrong (boot loop) because of that, U just disable overlay and U R back on with origial state. After U are satisfied with changes, U can merge those changes into read-only file system via recovery mode.
Sent from my HTC Legend
BlaY0, you're totally right. Overlay is a great thing for testing (and by the way many thanks you for what you did). But if you're not a tester, just an enthusiast who look for new stuff for his phone, overlay could be much more than he needs.
I'm looking for example to have as much free space in memory as possible. REAL free space. If I'm using overlay, that will not be gained right? The read only files will still be there, only the overlay will show them "deleted". So...what I'm doing instead is that I'm flashing one of the existing ROMs (as per my preferences - CM 6.1 RC1 for ex.) that will not "brick" my phone, I customize it with widgets and applications as I like, than I start deleting what I don't need. For sure I can use overlay for that, but I can do it also without it. This topic presented an alternative for doing that, to the known adb commands. Also from what I've understood, the method in this topic is more aimed to the ones that are not (or don't want to be) rooted. And for those, the adb method doesn't work
You sure are totally right, but then again if you deleted some apk from /system/app that is needed for some other apk and U didn't know about that, you could end up with a so called boot loop. And if this is done by some noob, the simplest way for him to restore would be to wipe and reflash the original ROM. Overay can prevent such accidents. Actually even with overlay you can save space especially where is needed the most, that's on data partition - there's no need for dex in dalvik-cache any more etc. and surely you get more free ram as that app isn't loading any more. For the system partition it actually doesn't matter if it is full in fact why it shouldn't be full. When we get our S-OFF the first thing I will do is to rearange mtd partitions shrinking system and extending data coz now I have like nearly 50 MB free on system partition that I can not use wisely.
Sent from my HTC Legend
Thanks, VF music and web app not banished from my Legend
Okay, I must be doing something wrong, but I have no idea what. I have the same ROM as Rapier on my Desire, I have Titanium Backup and I did everything he said above. The pre-installed apps are uninstalled with TB (Car app, News and Weather, Facebook, Twitter, Google Voice, Maps, Quickoffice 2.0 which I have no idea what really is), I clear the Dalvik cache and many mega are freed. Then if I reboot, they're back. Like nothing happened.
Do you have any idea or should I give more details? Thanks for the help, guys.
Have you checked also if those applications you're removing do not have some updates installed? Because if they do, you'll get them back on the phone. First remove the updates from each application (from normal "Application" management), then remove the application residing in system with TB.
PS. QuickOffice is a suite program similar with MS Office, that allows you to read (and in the paid version also to write) office documents (.doc, .xls, .ppt...etc)
Thank you for your quick reply.
Yes, I have checked and uninstalled all updates. They are all with the basic version.
About Quickoffice, I know what it is It's just that the one that came with CM 6.1.0 RC1 cannot be accessed, it can only be used to open supported file formats (I just found out after posting here ). I'd prefer the normal Quickoffice with which I can access my dropbox and Google docs too, that's why I wanted to uninstall this in the first place.

how to export installed list of applications to some file

Is there any way or any command which can save my installed set of applications to a Text file or PDF. My applications are growing and I cannot remember every one of them and I require all of them at one point or other. Can anyone give me some guidance?
You could use titanium backup, it does have an option to create an update.zip file for your backups which I haven't used but I assume it backs up your apps to the zip so you can reinstall apps from recovery, would need someone to clarify this though
Sent from my GT-I9000 using XDA App
I was using back up pro but it is no use. Suppose you flash a new rom, and if you restore most of them end up with Force Close errors. Since most of my applications are free, I don't mind spending some time installing them. But since many roms are changing so fast, I have to flash to keep up with the times, you know.
I don't know if there is such an option to save a list of installed apps, but it would be kinda useful.
I soon realized such a list would help and I am just manually creating my own in a text file, and all of the non-stock apps I have (thus far) added are in appbrain.com and I have ensured I have added each to "Apps on the phone" which then appears under "My Apps".
A list no but as all my apps are via AppBrain that's my list .
I use Root Explorer to copy all the APKS to a folder on the external card + a copy on PC . New firmware just open APK folder and install .
jje
For the time being, I am using Titanium free version and it backed up my applications and after I flashed the new rom I was able to restore all the applications via it's batch run commands. I do hope that I don't get force close errors. Upto now everything is working fine.
Thanks to all for your kind replies

[TOOL]Semi-auto bloatware remover for Xperia pro et al v0.1

I made a simple script for my own use that does pretty much the same job as Knight47's auto bloatware remover.
The main difference is that mine reads the list of removed apps from a separate text-file that can be adjusted to taste.
Root required!
How to use:
1. Backup your phone with nandroid!
2. Unzip zip-file to some folder
3. Connect USB cable to phone and make sure USB debugging is turned on
4. Run debloat.cmd
5. Reboot
6. Enjoy fat-free phone
It MIGHT be necessary to clean Dalvik-cache afterwards if the phone does not rebuild dalvik cache automagically ("updating android"-message during reboot)
I wrote this for Xperia Pro Mk16i ICS, which had some differences from the main APP-list:
SEMCFacebookProxy.apk --- appears to be more facebook stuff
livewaremanager.apk -- all in lower-case now
letsgolf_i.apk -- filename has changed
Also some files listed in the app collection did not exist here. ALL files from main Xperia arc app list are included anyways.
I'm removing:
Browser.apk
facebook.apk
Gmail.apk
GMS_Maps.apk
Maps.apk
Street.apk
YouTube.apk
These apps take double space after you install updates for them so it makes sense to remove them from system. If you already have updated them, there's no need to do anything, otherwise download them from play store.
With regards to stock browser, if you don't have chrome or similar, just comment it out.
..
Changes in v0.2:
Fixed script syntax
Delete .apk and .odex files
Added some files to kill-list:
weatherwidget
com.google.android.youtube-1
SemcCamera3D
SemcSnpVideoPlayer
Semcsdnla
Wait for keypress after finished + reboot into recovery to clean dalvik.
v0.21
Do not delete google maps and youtube app by default, change advisor text
nothing happened. i have rooted phone and busybox
my bloat.txt is something like this(only apps, no cements)
EventStream.apk
EventStreamPluginCallLog.apk
EventStreamPluginFacebook.apk
EventStreamPluginTelephony.apk
EventStreamPluginTwitter.apk
usb conection mode is mass storagemode
ics 4.0.4
seljachina said:
nothing happened. i have rooted phone and busybox
my bloat.txt is something like this(only apps, no cements)
EventStream.apk
EventStreamPluginCallLog.apk
EventStreamPluginFacebook.apk
EventStreamPluginTelephony.apk
EventStreamPluginTwitter.apk
usb conection mode is mass storagemode
ics 4.0.4
Click to expand...
Click to collapse
Are those files in /system/app ? You have ADB drivers installed?
What exactly happens when "nothing happens"? Can you start the script from cmd and tell me what it says?
yes those are apps from /system/app
here is a screenshot of cmd(cmd window is auto closed 1-2 seconds after i run debload.cmd)
on phone is displayed "shell has been granted superuser permission"
can i edit bload.txt in notepad or another text editor?
seljachina said:
yes those are apps from /system/app
here is a screenshot of cmd(cmd window is auto closed 1-2 seconds after i run debload.cmd)
on phone is displayed "shell has been granted superuser permission"
can i edit bload.txt in notepad or another text editor?
Click to expand...
Click to collapse
That's the whole idea, you can edit it. Did you? It looks like the bloat.txt is not in the right place or perhaps has empty lines or something..
command prompt stays open if you run cmd.exe from start menu. Or ctrl-right click on a folder and "open command window here"
yes i did
i notice the difference.. your adb.exe is about 2mb, my adb.exe is 150kb?! maybe that is problem, some drivers.. who knows. (when i try with my adb.exe, it just say "waiting for device").. i manually remove bloatware
I upgraded into omega rom recently that retains some of the cruft in stock rom. So I updated my debloater. Script has been revised to actually work , I must have attached a wrong version by mistake. It now also wipes out .odex files if present. Because of this, deleted filenames are without extension (.apk) in bloat.txt.
To make this really elegant, files should be actually un-installed as now there may be some libraries and data left behind. I'm not going to trace down package name for each and every sony bloatware today, though.
Finally, dalvik cache needs to be wiped to remove the orphaned odex cache files which take most of the space.
It is actually possible to reclaim a lot of space by using titanium backup to integrate some large apps into ROM. Preferably those which do not allow you to move them into sdcard and/or work badly if linked with link2sd. In my phone I have 130MB of free space in the system partition so Chrome alone gives a big chunk of free space for other apps.
After thinking this through, there is NO benefit into removing system apps if you're going to reinstall them from play store anyways. It's better to use titanium backup to integrate any updates into ROM which actually gives more room for apps. I removed google maps and youtube from being deleted by default. Some people may want to edit bloat.txt for facebook and gmail app as well.
Bash script port for linux users
This might not be useful for many people, but I use Linux and I converted this script to work with bash.
Download and run the script as su or sudo.

Integrate Updated System Apps

Hi there i have 4.0.2 rooted working right now but i like to integrate the updates of system apps to have some space. I have been doing it with all my phones and all android versions with rooted and r/w system parts file managers by copy&paste and giving right permissions (644) but i understand that something changed in nougat the way system apps are handled. when i push an apk as a system app and reboot, app disappears even if i gave right permissions. Some apps have libs and odex files also. For example Google Play Store app appears as /system/priv-app/Phonesky/Phonesky.apk but updated version is in data/app/com.android.vending-1 which contains lib and oat folders and base.apk. i used to copy just the apk file in exchange of phonesky.apk and chmod 644 reboot and go! that doesn't work anymore. i tried several apps like link2sd and system file mover, they won't work too. thanks for any help.
I figured how, and want to reply my own question
tried open gapps aroma installer and selected the ones that i want to remain and gapps did the rest. now my device has no updated system google apps. instead all gapps are under system.
AFAIK Titanium Backup has an option to intergrate system apps updates to /system

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