[07.09.2012][CF-Root 5.6] K**,LA-1346,LB1,LC1,LP-1YF89,LQ-23,LR-GIKQ - su+bb+CWM5

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Chainfire

Moderator Emeritus / Senior Recognized Developer
Oct 2, 2007
11,452
87,862
www.chainfire.eu
This rooted kernel is for the "rooting beginners" and those who want to keep as close to stock as possible. CF-Root takes the kernel from an original Samsung firmware, and just adds root, busybox, and ClockWorkMod recovery

THIS IS NOT A ROM - it is only a modified kernel. You need to have the relevant firmware already on your device. You do NOT need to wipe anything for this patch. You DO need to read the instructions. PLEASE READ THE ENTIRE FIRST FEW POSTS!

Donate
There have now been nearly 1.000.000 downloads of CF-Root for various devices (see for example Galaxy S1, Galaxy Tab 7", and Galaxy S2), and many more if you include ROMs, kernels, etc that use it. Don't be a leech, buy me a beer (and use the "Thanks" button!). Imagine if every CF-Root user had donated me $1... :)

Main features
- The kernel is fully stock and taken from the original firmware, with just the following added:
- Root
- Busybox v1.19.2-cm71
- ClockWorkMod Recovery 5
- CWM Manager (see below for more detail)
- Custom boot / init scripts
- Custom boot animations

v5.3 and newer
- SuperSU (replaces Superuser)
- "Fake-secure" (ro.secure=1, but ADB is patched to run as ro.secure=0)

v5.5 and newer
- CWM updated to v5.5

v5.6 and newer
- Possible brickbug fix

Installation instructions
Please see the next post !

Other kernels
Replacing CF-Root with other kernels and vice-versa sometimes works, sometimes it doesn't. I don't have a list.

When going from CF-Root to another kernel, root will usually stay, while CWM will be lost (unless the other kernel also includes it), but there should not be issues. The CWM Manager app may remain, but probably won't do anything useful.

ClockworkMod
CF-Root includes a custom version of CWM5. I always make custom versions, as the originals often do not take some Samsung specific things into account.

CF-Root/CWM5 is NOT compatible with ROM Manager! Manage/perform your backup/restores from CWM directly or using the CWM Manager application included with CF-Root

- Booting into recovery will immediately give you CWM. The standard recovery will only be started if a Samsung package is detected.
- ADB is functional in recovery, however it may take up to a minute for it to start up after booting into recovery.

CWM Manager
Because of incompatibilities with ROM Manager, I wrote and included "CWM Manager". This is a new app (as of March 30, 2011). You can find it under Applications -> CWM. It is much faster to use than manually booting into CWM and selecting these options.

Features:
- Boot to ClockWorkMod Recovery
- Boot to Download mode
- Reboot normally
- Backup firmware
- Restore backups (including partition selection)
- Delete backups
- Install APKs
- Flash CWM3/4/5 update.zip's
- Flash kernels (zImage, zImage in TAR, zImage in ZIP, zImage in TAR in ZIP)
--- without changing warning triangle status or increasing flash counter
- Flash complete firmwares (seperate files as well as .tar and .tar.md5 archives, dump files in /sdcard/external_sd/firmware folder)
--- without changing warning triangle status or increasing flash counter
--- can pre-root new firmwares during flash

Note: If you flash a different kernel, CWM Manager may remain installed. However, functions may not work, because they need kernel compatibility !

Custom boot / init scripts
CF-Root will execute the following scripts if present, in the order listed:

- /system/etc/init.d/* (there can be many files here, no extensions! use #!)
- /system/bin/customboot.sh (busybox sh)
- /system/xbin/customboot.sh (busybox sh)
- /data/local/customboot.sh (busybox sh)

Please make sure you chown / chmod the scripts correctly so they can be executed. Pretty much root:root / 755.

Custom boot animations and binaries
CF-Root also supports custom boot animations:

- /system/media/bootanimation.zip
- /data/local/bootanimation.zip

And custom boot binaries:

- /data/local/bootanimation.bin

Installing busybox over the included version
It is possible to install a custom busybox over CF-Root v3.0 and newer. However, this is not without risk. CF-Root makes heavy use of scripting, and many CF-Root scripts rely on the internal busybox version. If you do install a seperate busybox version (always use "stericson" installer!), install it to /system/xbin. Installing it to /system/bin will mess things up for sure. Even if you do that part right, it may still break CF-Root, so make sure to make a backup before trying.

How ?
I wrote my own toolchain to ease patching of initramfs, and that is what all this is based on. It is now used to make CF-Root for many devices!

Help! Which file do I use ?
Listen closely, for I will say zis only once!

Go to Settings -> About phone -> Kernel Version. Note the string present there:

2.6.35.7-N7000XXKJ4-CL641703

What matters most (KJ4) in this case, is in bold. Try to find the matching file under downloads:

CF-Root-SGN_XX_XEN_KJ4-v5.0-CWM4.zip

The XX and XEN identifiers are not that important. Usually a "KJ4" kernel is a "KJ4" kernel, and that is that. Sometimes (pretty rare) it happens there will be multiple different kernels with the same name in different firmwares, that are actually different. If this happens, they are usually only very minor changes and you should expect them to still be fully compatible. I include the "XX" and "XEN" identifiers so the very advanced users can deduce from which full firmware I have taken the kernel file.

Don't worry too much, just find the matching download and use it. What if there is no matching download ? You can ask me to make one, but I can tell you right now, I very very rarely make CF-Root's for kernels on request, unless it is the very latest kernel that has been released by Samsung. In the latter case, be sure to let me know. If there's no match and I'm not making one, try finding the closest match. You should treat "KJ4" as a number, but instead of 1-9, we have 1-9, A-Z (where A would be 10, and Z would be 35). "KJ3" is really close to "KJ4", "KF1" is not close to "KG4" at all. I hope that makes sense.

@Developers: I have noticed that doing a NANDROID RESTORE while connected to your computer AND Eclipse is running may cause the restore to fail. Eclipse automatically starts logcatting in the background, which will prevent /system from being properly restored.

Download
These are general-purpose downloads. See the posts following this one for the kernels.
 

Attachments

  • Odin3-v1.85.zip
    198.4 KB · Views: 112,147
Last edited:

Chainfire

Moderator Emeritus / Senior Recognized Developer
Oct 2, 2007
11,452
87,862
www.chainfire.eu
Installation intructions

The Samsung Galaxy Note keeps track of the kind of kernel you are running (stock or custom) and how often you have flashed kernels. This is probably for warranty purposes. There is currently no known way to reset this counter on the SGN.

So, what we want to do is get root, busybox, and CWM, all without getting that ugly yellow triangle or updating the flash counter on our device. Luckily, CF-Root allows for all these things. The new CWM Manager even allows you to flash new firmwares and apply root to them while flashing.

We need to get rid of ODIN pretty much completely, and we can! The difficult part is getting root the first time, after that, it should be happy camping forever.

--- Chapter 1: Initial application of root ---

DO NOT USE ODIN TO FLASH THE KERNEL !

This is the annoying part. There are three different methods:

1.1. If you are already rooted

- Download the attached "InitialRootFlasher.zip" and extract it somewhere
- Download one of the CF-Root kernels, and extract it (repeat) until you end up with a zImage file
- Place the zImage file from the CF-Root kernel in the zImage folder from InitialRootFlasher
- Start "already-rooted.bat" and follow the instructions

For those needing to do this manually (Linux boxes and such), this is the important command. Place the zImage file on your phone (example: /data/local/zImage) and execute this command in a rooted shell:
dd if=/data/local/zImage of=/dev/block/mmcblk0p5 bs=4096

1.2. If you are not rooted yet: Using the zergRush exploit This method no longer works on KL* and newer firmwares!

(while it still works on our firmwares, this exploit will probably be fixed soon! Known to work on KJ1 and KJ4 firmwares)

- Download the attached "InitialRootFlasher.zip" and extract it somewhere
- Download one of the CF-Root kernels, and extract it (repeat) until you end up with a zImage file
- Place the zImage file from the CF-Root kernel in the zImage folder from InitialRootFlasher
- Start "not-rooted-yet.bat" and follow the instructions

1.3. If you are not rooted yet: Flash a modified FACTORYFS

I am providing this method just this once, for the KJ1 firmware. This is the /system part of the KJ1 firmware, modified so at first boot it will flash the KJ1 CF-Root and reboot, without getting you the yellow triangle or increasing the flash counter.

Using a newer firmware? Do this operation first, then flash the newer firmware back using CWM Manager. This is explained in Chapter 3 below.

Download: http://www.multiupload.com/YB9EL8D8O3

- Optional: flash the full KJ1 firmware first
- Unzip the file, you should get "SGN_XX_OXA_KJ1_FACTORYFS.tar"
- Make sure your SGN is NOT connected to your computer
- Reboot your SGN into "download mode" (see below)
- Start ODIN
- Click the PDA button, and select the "SGN_XX_OXA_KJ1_FACTORYFS.tar" file
- Connect the SGN to your computer
- Make sure "repartition" is NOT checked
- Click the START button
- Wait for the phone to reboot TWICE
- Done

If you do not know how to get into download mode:
- Turn off the device
- Count to 10
- Hold the "home" (the big physical button in the middle) and "volume down" buttons
- Press and release the power button (keep holding "home" and "volume down" !) to turn the device on
- You should get a download mode screen
- If it tells you to press a button to continue, do so

--- Chapter 2: Getting rid of ODIN ---

This is easy. Find ODIN, and delete it. In the future you should only need it to flash bootloaders, which probably will only really be needed one time: when upgrading from Gingerbread to Ice Cream Sandwich.

--- Chapter 3: Upgrading your firmware ---

My CWM Manager application has a full-fledged firmware flasher built in. Using the flasher from CWM Manager does NOT give you the yellow triangle or increase the flash counter.

3.1. Flashing a new kernel

This is easy. CWM Manager can flash zImage files (on any rooted kernel), zImage files inside a .tar file (only on a CF-Root kernel), and zImage files inside a .tar.zip (only on a CF-Root kernel). Note that zImage must be the ONLY file in an archive, if is is inside a tar or zipped tar.

- Put the zImage (or tar, or zip) file on your SD card
- Open the CWM Manager app
- Select "Flash kernel"
- Select the file you just put on your device
- CWM Manager will flash the kernel and reboot

If you flash a non-CF-Root kernel, you will lose a lot of functionality from CWM Manager. However, the app will (likely) still allow you to flash kernels.

3.2. Flashing a new firmware

Important: This works ONLY on a CF-Root kernel !

CWM Manager has the ability to flash firmware parts either from separate files (zImage, factoryfs.img, etc) or from .tar / .tar.md5 files that they usually come packaged in.

- Download the firmware you want to flash
- If you have a ZIP or RAR file, extract it until you have seperate files, or .tar / .tar.md5 files
- Create a folder named 'firmware' on your external SD card
- Copy the files you want to flash to this folder ( /sdcard/external_sd/firmware ). factoryfs ("system") is mandatory part at the moment.
- TIP: If you are flashing a new firmware that already has a CF-Root kernel available, put it in the 'firmware' folder as well in zImage or .tar form (NOT .zip). Select it when asked which kernel to use, then use the "Flash normally" option later on.
- Open the CWM Manager app
- Select "Flash stock firmware"

- At this point, CWM Manager will tell you about the firmware parts it has found, and which ones it will flash. It will also give you warnings about bootloaders and PIT files if those were found. If some firmware parts are present multiple times, it will ask you which file to use as source.

- If what you are flashing includes both kernel and system parts, CWM Manager will warn you about this as you are about to lose root. It will provide you with three options:

1: Keep CF-Root kernel
Keeps the current CF-Root kernel, only flash the other parts. You will not lose root or CWM Recovery. You can flash a newer CF-Root kernel later (or maybe you have already done so), see 3.1 above.

2: Pre-root system
Flashes both kernel and system parts, but roots system during the flash. You will lose CWM Recovery, but you will keep root (if all goes well). The CWM Manager application will also remain, and allow you to flash the correct CF-Root kernel at a different time (if you have not done so before), see 3.1 above.

3: Flash normally
Doesn't do anything specific. If the kernel you are flashing is not a CF-Root (or similar) kernel, you will lose root, and CWM Recovery.

- CWM Manager will reboot into CWM Recovery, and will flash the firmware, rebooting afterwards.
 

Attachments

  • InitialCFRootFlasher.zip
    791.6 KB · Views: 100,135
Last edited:

Chainfire

Moderator Emeritus / Senior Recognized Developer
Oct 2, 2007
11,452
87,862
www.chainfire.eu

Chainfire

Moderator Emeritus / Senior Recognized Developer
Oct 2, 2007
11,452
87,862
www.chainfire.eu
Z

zylor

Guest
Will buy a note! Thz Chainfire :D

Sent from my GT-I9100 using xda premium
 

walda

Senior Member
Apr 2, 2010
1,387
249
I'm also glad to see you on this device too. Thanks man!

sent from my Galaxy Note via T*patalk
 
  • Like
Reactions: cdyangren

adnan.makarevic

Senior Member
Nov 9, 2009
472
82
44
Nothing Phone 2
nice to see you here.. ;) short question regardin binary counter, usb jig didnt work, is there a way to flash your kernel whitout affect the binary counter?

Should be ready later tonight or early tomorrow. I need the thread URL :)

(could have posted it days ago, but I'm still fixing minor issues with CWM5)

Usual CF-Root features apply. Root, busybox, CWM, custom bootanimations, custom boot scripts, CWM Manager(tm), etc.
 

RavenY2K3

Senior Member
Nov 13, 2006
1,459
439
I always know when I've bought the right device when I see you pop up the same forum :)

Sent from my GT-N7000 using Tapatalk
 

zion12

Senior Member
Nov 12, 2008
93
5
Pune
Can't wait for this. Any idea what file system the Note uses?

Sent from my GT-I9000 using xda premium
 
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  • 502
    This rooted kernel is for the "rooting beginners" and those who want to keep as close to stock as possible. CF-Root takes the kernel from an original Samsung firmware, and just adds root, busybox, and ClockWorkMod recovery

    THIS IS NOT A ROM - it is only a modified kernel. You need to have the relevant firmware already on your device. You do NOT need to wipe anything for this patch. You DO need to read the instructions. PLEASE READ THE ENTIRE FIRST FEW POSTS!

    Donate
    There have now been nearly 1.000.000 downloads of CF-Root for various devices (see for example Galaxy S1, Galaxy Tab 7", and Galaxy S2), and many more if you include ROMs, kernels, etc that use it. Don't be a leech, buy me a beer (and use the "Thanks" button!). Imagine if every CF-Root user had donated me $1... :)

    Main features
    - The kernel is fully stock and taken from the original firmware, with just the following added:
    - Root
    - Busybox v1.19.2-cm71
    - ClockWorkMod Recovery 5
    - CWM Manager (see below for more detail)
    - Custom boot / init scripts
    - Custom boot animations

    v5.3 and newer
    - SuperSU (replaces Superuser)
    - "Fake-secure" (ro.secure=1, but ADB is patched to run as ro.secure=0)

    v5.5 and newer
    - CWM updated to v5.5

    v5.6 and newer
    - Possible brickbug fix

    Installation instructions
    Please see the next post !

    Other kernels
    Replacing CF-Root with other kernels and vice-versa sometimes works, sometimes it doesn't. I don't have a list.

    When going from CF-Root to another kernel, root will usually stay, while CWM will be lost (unless the other kernel also includes it), but there should not be issues. The CWM Manager app may remain, but probably won't do anything useful.

    ClockworkMod
    CF-Root includes a custom version of CWM5. I always make custom versions, as the originals often do not take some Samsung specific things into account.

    CF-Root/CWM5 is NOT compatible with ROM Manager! Manage/perform your backup/restores from CWM directly or using the CWM Manager application included with CF-Root

    - Booting into recovery will immediately give you CWM. The standard recovery will only be started if a Samsung package is detected.
    - ADB is functional in recovery, however it may take up to a minute for it to start up after booting into recovery.

    CWM Manager
    Because of incompatibilities with ROM Manager, I wrote and included "CWM Manager". This is a new app (as of March 30, 2011). You can find it under Applications -> CWM. It is much faster to use than manually booting into CWM and selecting these options.

    Features:
    - Boot to ClockWorkMod Recovery
    - Boot to Download mode
    - Reboot normally
    - Backup firmware
    - Restore backups (including partition selection)
    - Delete backups
    - Install APKs
    - Flash CWM3/4/5 update.zip's
    - Flash kernels (zImage, zImage in TAR, zImage in ZIP, zImage in TAR in ZIP)
    --- without changing warning triangle status or increasing flash counter
    - Flash complete firmwares (seperate files as well as .tar and .tar.md5 archives, dump files in /sdcard/external_sd/firmware folder)
    --- without changing warning triangle status or increasing flash counter
    --- can pre-root new firmwares during flash

    Note: If you flash a different kernel, CWM Manager may remain installed. However, functions may not work, because they need kernel compatibility !

    Custom boot / init scripts
    CF-Root will execute the following scripts if present, in the order listed:

    - /system/etc/init.d/* (there can be many files here, no extensions! use #!)
    - /system/bin/customboot.sh (busybox sh)
    - /system/xbin/customboot.sh (busybox sh)
    - /data/local/customboot.sh (busybox sh)

    Please make sure you chown / chmod the scripts correctly so they can be executed. Pretty much root:root / 755.

    Custom boot animations and binaries
    CF-Root also supports custom boot animations:

    - /system/media/bootanimation.zip
    - /data/local/bootanimation.zip

    And custom boot binaries:

    - /data/local/bootanimation.bin

    Installing busybox over the included version
    It is possible to install a custom busybox over CF-Root v3.0 and newer. However, this is not without risk. CF-Root makes heavy use of scripting, and many CF-Root scripts rely on the internal busybox version. If you do install a seperate busybox version (always use "stericson" installer!), install it to /system/xbin. Installing it to /system/bin will mess things up for sure. Even if you do that part right, it may still break CF-Root, so make sure to make a backup before trying.

    How ?
    I wrote my own toolchain to ease patching of initramfs, and that is what all this is based on. It is now used to make CF-Root for many devices!

    Help! Which file do I use ?
    Listen closely, for I will say zis only once!

    Go to Settings -> About phone -> Kernel Version. Note the string present there:

    2.6.35.7-N7000XXKJ4-CL641703

    What matters most (KJ4) in this case, is in bold. Try to find the matching file under downloads:

    CF-Root-SGN_XX_XEN_KJ4-v5.0-CWM4.zip

    The XX and XEN identifiers are not that important. Usually a "KJ4" kernel is a "KJ4" kernel, and that is that. Sometimes (pretty rare) it happens there will be multiple different kernels with the same name in different firmwares, that are actually different. If this happens, they are usually only very minor changes and you should expect them to still be fully compatible. I include the "XX" and "XEN" identifiers so the very advanced users can deduce from which full firmware I have taken the kernel file.

    Don't worry too much, just find the matching download and use it. What if there is no matching download ? You can ask me to make one, but I can tell you right now, I very very rarely make CF-Root's for kernels on request, unless it is the very latest kernel that has been released by Samsung. In the latter case, be sure to let me know. If there's no match and I'm not making one, try finding the closest match. You should treat "KJ4" as a number, but instead of 1-9, we have 1-9, A-Z (where A would be 10, and Z would be 35). "KJ3" is really close to "KJ4", "KF1" is not close to "KG4" at all. I hope that makes sense.

    @Developers: I have noticed that doing a NANDROID RESTORE while connected to your computer AND Eclipse is running may cause the restore to fail. Eclipse automatically starts logcatting in the background, which will prevent /system from being properly restored.

    Download
    These are general-purpose downloads. See the posts following this one for the kernels.
    188
    Installation intructions

    The Samsung Galaxy Note keeps track of the kind of kernel you are running (stock or custom) and how often you have flashed kernels. This is probably for warranty purposes. There is currently no known way to reset this counter on the SGN.

    So, what we want to do is get root, busybox, and CWM, all without getting that ugly yellow triangle or updating the flash counter on our device. Luckily, CF-Root allows for all these things. The new CWM Manager even allows you to flash new firmwares and apply root to them while flashing.

    We need to get rid of ODIN pretty much completely, and we can! The difficult part is getting root the first time, after that, it should be happy camping forever.

    --- Chapter 1: Initial application of root ---

    DO NOT USE ODIN TO FLASH THE KERNEL !

    This is the annoying part. There are three different methods:

    1.1. If you are already rooted

    - Download the attached "InitialRootFlasher.zip" and extract it somewhere
    - Download one of the CF-Root kernels, and extract it (repeat) until you end up with a zImage file
    - Place the zImage file from the CF-Root kernel in the zImage folder from InitialRootFlasher
    - Start "already-rooted.bat" and follow the instructions

    For those needing to do this manually (Linux boxes and such), this is the important command. Place the zImage file on your phone (example: /data/local/zImage) and execute this command in a rooted shell:
    dd if=/data/local/zImage of=/dev/block/mmcblk0p5 bs=4096

    1.2. If you are not rooted yet: Using the zergRush exploit This method no longer works on KL* and newer firmwares!

    (while it still works on our firmwares, this exploit will probably be fixed soon! Known to work on KJ1 and KJ4 firmwares)

    - Download the attached "InitialRootFlasher.zip" and extract it somewhere
    - Download one of the CF-Root kernels, and extract it (repeat) until you end up with a zImage file
    - Place the zImage file from the CF-Root kernel in the zImage folder from InitialRootFlasher
    - Start "not-rooted-yet.bat" and follow the instructions

    1.3. If you are not rooted yet: Flash a modified FACTORYFS

    I am providing this method just this once, for the KJ1 firmware. This is the /system part of the KJ1 firmware, modified so at first boot it will flash the KJ1 CF-Root and reboot, without getting you the yellow triangle or increasing the flash counter.

    Using a newer firmware? Do this operation first, then flash the newer firmware back using CWM Manager. This is explained in Chapter 3 below.

    Download: http://www.multiupload.com/YB9EL8D8O3

    - Optional: flash the full KJ1 firmware first
    - Unzip the file, you should get "SGN_XX_OXA_KJ1_FACTORYFS.tar"
    - Make sure your SGN is NOT connected to your computer
    - Reboot your SGN into "download mode" (see below)
    - Start ODIN
    - Click the PDA button, and select the "SGN_XX_OXA_KJ1_FACTORYFS.tar" file
    - Connect the SGN to your computer
    - Make sure "repartition" is NOT checked
    - Click the START button
    - Wait for the phone to reboot TWICE
    - Done

    If you do not know how to get into download mode:
    - Turn off the device
    - Count to 10
    - Hold the "home" (the big physical button in the middle) and "volume down" buttons
    - Press and release the power button (keep holding "home" and "volume down" !) to turn the device on
    - You should get a download mode screen
    - If it tells you to press a button to continue, do so

    --- Chapter 2: Getting rid of ODIN ---

    This is easy. Find ODIN, and delete it. In the future you should only need it to flash bootloaders, which probably will only really be needed one time: when upgrading from Gingerbread to Ice Cream Sandwich.

    --- Chapter 3: Upgrading your firmware ---

    My CWM Manager application has a full-fledged firmware flasher built in. Using the flasher from CWM Manager does NOT give you the yellow triangle or increase the flash counter.

    3.1. Flashing a new kernel

    This is easy. CWM Manager can flash zImage files (on any rooted kernel), zImage files inside a .tar file (only on a CF-Root kernel), and zImage files inside a .tar.zip (only on a CF-Root kernel). Note that zImage must be the ONLY file in an archive, if is is inside a tar or zipped tar.

    - Put the zImage (or tar, or zip) file on your SD card
    - Open the CWM Manager app
    - Select "Flash kernel"
    - Select the file you just put on your device
    - CWM Manager will flash the kernel and reboot

    If you flash a non-CF-Root kernel, you will lose a lot of functionality from CWM Manager. However, the app will (likely) still allow you to flash kernels.

    3.2. Flashing a new firmware

    Important: This works ONLY on a CF-Root kernel !

    CWM Manager has the ability to flash firmware parts either from separate files (zImage, factoryfs.img, etc) or from .tar / .tar.md5 files that they usually come packaged in.

    - Download the firmware you want to flash
    - If you have a ZIP or RAR file, extract it until you have seperate files, or .tar / .tar.md5 files
    - Create a folder named 'firmware' on your external SD card
    - Copy the files you want to flash to this folder ( /sdcard/external_sd/firmware ). factoryfs ("system") is mandatory part at the moment.
    - TIP: If you are flashing a new firmware that already has a CF-Root kernel available, put it in the 'firmware' folder as well in zImage or .tar form (NOT .zip). Select it when asked which kernel to use, then use the "Flash normally" option later on.
    - Open the CWM Manager app
    - Select "Flash stock firmware"

    - At this point, CWM Manager will tell you about the firmware parts it has found, and which ones it will flash. It will also give you warnings about bootloaders and PIT files if those were found. If some firmware parts are present multiple times, it will ask you which file to use as source.

    - If what you are flashing includes both kernel and system parts, CWM Manager will warn you about this as you are about to lose root. It will provide you with three options:

    1: Keep CF-Root kernel
    Keeps the current CF-Root kernel, only flash the other parts. You will not lose root or CWM Recovery. You can flash a newer CF-Root kernel later (or maybe you have already done so), see 3.1 above.

    2: Pre-root system
    Flashes both kernel and system parts, but roots system during the flash. You will lose CWM Recovery, but you will keep root (if all goes well). The CWM Manager application will also remain, and allow you to flash the correct CF-Root kernel at a different time (if you have not done so before), see 3.1 above.

    3: Flash normally
    Doesn't do anything specific. If the kernel you are flashing is not a CF-Root (or similar) kernel, you will lose root, and CWM Recovery.

    - CWM Manager will reboot into CWM Recovery, and will flash the firmware, rebooting afterwards.