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Root Welcome to Jelly Bean - Rooting

If you're running Linux this can be done in VirtualBox it's actually quite easy, you'll need to enable USB, do a Google search for "how to enable usb virtualbox linux", you'll need to download VirtualBox extention (it's free now, you use to have to pay for it), then add your username to vboxusers (Google "how to add user to groups linux"), then log out and back in, startup VirtualBox, go to the settings for your Windows virtual machine, down to USB, check BOTH boxes for USB support, hit OK, launch your Windows virtual machine, when it loads go to the bottom of the screen where you see a little USB icon (on the bottom of the VirtualBox window, not the Windows task bar in the virtual machine), when you click on it you should see a long list of USB devices, if you phone is plugged in it should be there, once the Windows virtual machine is recognizing the phone just follow the instructions from bkttk2.

I know that's a real quick run down, but most Linux users should be able to follow (at least I hope :/ ). I would post an actual tutorial but I really don't have the time, if anyone (who is actually running Linux) finds this too confusing and would like me to post a better tutorial just say so and I'll work it into my schedule.
 
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Thank you everyone for the help! This is the first time I have flashed a phone.

I thought it was worth mentioning that for whatever reason, when I went to boot into recovery mode, holding VOL-UP + POWER did not work for me. Doing that only made my phone flash the black Samsung screen with the words "boot to recovery mode by key" in the corner. I got into to actual recovery mode by holding down the power button by itself.
 
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That's a lot of information. I'm feeling a little overwhelmed.

I'm already rooted and I have things symlinked to my external SD card. (I can unlink them pretty easily if I have to.) The phone has been pestering me for several days that there's a system update. I tried allowing it the first time, but it booted into what looked like recovery or something, and I wasn't sure what I was supposed to do, so I backed out without allowing any changes.

If someone could narrow things down for me, I'd appreciate it.

Thanks.
 
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Sorry. Yes, I'm using the ROM that the phone came with (ICS). I followed mystichunter's instructions on how to root with Poot. I don't know what you mean by "baseband" though.

Thanks.

Baseband is by Android version on about phone under system settings.

Did you remove any stock files?

If you only rooted you should be able to follow force update in OP. Accept download and let it install. You will need to unlink all apps as you will lose root. After update you can follow root process in OP.
 
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Baseband is by Android version on about phone under system settings.

Did you remove any stock files?

If you only rooted you should be able to follow force update in OP. Accept download and let it install. You will need to unlink all apps as you will lose root. After update you can follow root process in OP.

I have not removed any stock files. I'm using stock ICS 4.0.4 baseband version M950VPMB3.

I'll post my progress so I don't get confused and make a mistake.

Thanks.
 
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Sadly, that link seems to be broken. I assume this is the set of directions I should be following.

I updated the OP. Here is the info you need.

To Force the Jelly Bean Update see comments by 13jpgbass:

Force OTA update

If you want to force the update go to application manager>all>google service frameworks>clear data>force stop and then check for updates again, and it should (should) push the update.
 
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Does the JB update replace the recovery with a JB-version of recovery?

The reason I ask is that I previously installed CWM recovery when the phone was running ICS and it was my understanding that stock recovery was required in order for the official JB update to succeed. So I reinstalled the stock recovery (from xInterlopeRx http://androidforums.com/reverb-all-things-root/657374-oudhs-soft-brick-cwm-recovery-support.html) before the JB update.

Now it looks like I'll have to re-install CWM recovery in order to get root access under JB. So my concern is that if I ever need to go back to stock recovery, will the stock recovery from when the phone was on ICS work?
 
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Does the JB update replace the recovery with a JB-version of recovery?

The reason I ask is that I previously installed CWM recovery when the phone was running ICS and it was my understanding that stock recovery was required in order for the official JB update to succeed. So I reinstalled the stock recovery (from xInterlopeRx http://androidforums.com/reverb-all-things-root/657374-oudhs-soft-brick-cwm-recovery-support.html) before the JB update.

Now it looks like I'll have to re-install CWM recovery in order to get root access under JB. So my concern is that if I ever need to go back to stock recovery, will the stock recovery from when the phone was on ICS work?

Good question. Unfortunately I do not know the answer. My first response is it should work but I honestly don't know.
 
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I have not removed any stock files. I'm using stock ICS 4.0.4 baseband version M950VPMB3.

I'll post my progress so I don't get confused and make a mistake.

Thanks.

All right. So I told my phone I was ready to install the update. It rebooted, and now I've got the green android guy standing there with his belly open and a blue shape floating in his belly.

Code:
Install Untrusted Package?
   THIS CAN NOT BE UNDONE.

-----------------
- No
- No
- No
- No
- No
- No
- No
- Yes - Install untrusted zip
- No
- No
- No
- +++++ Go Back +++++
-----------------

CWM-based Recovery v6.0.2.3
E: Invalid command argument
Finding update package...
Opening update package...
Verifying update package...
E: failed to verify whole-file signature
E: signature verification failed
I'm not sure if this is what it's supposed to look like or not. If all is well at this point, tell me yes and I'll select "Yes - Install untrusted zip." Otherwise, tell me no and I'll back out.

Thanks.
 
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