[Nexus 10 Android Development] Zixin:
Turns out my problem was more complicated than I thought. I discovered I had no custom recovery and probably no full root although it appeard to be OK. Any attempts to go into recovery ended in the stock revovery screen (lying down amdroid with !) but no command text.

I managed to manually fastboot flash LMY48M, then using your tool tried to root again, same result, several attempts later (flash stock & unroot + root) I decided to try another tool for root which succeeded. (with SuperSu 2.46). It's the fist time ever I have experienced any issue like this, here is part log from the rooting bit:

Checking Fastboot Connectivity

fastboot devices

R32D100SMLT	fastboot

Connectivity Status: Fastboot Device Connected

+ Confirmed: Bootloader Unlocked.

Flashing Custom Recovery to RECOVERY partition...

fastboot flash recovery "C:\Program Files (x86)\WugFresh Development\Nexus Root Toolkit\data\Recovery_Custom\TWRP\twrp-2.8.7.0-manta.img"

Temporarily Booting modified boot.img to enable running privileged commands...

fastboot boot "C:\Program Files (x86)\WugFresh Development\Nexus Root Toolkit\data\Modified_Boot\modified_boot_mantaray_5.1.1_LMY48M.img"

Waiting for your device...

Device Detected

Pushing root files to your device...

Pushing "BETA-SuperSU-v2.52.zip" to your device...

adb push "C:\Program Files (x86)\WugFresh Development\Nexus Root Toolkit\data\Root_Files\BETA-SuperSU-v2.52.zip" "/sdcard/!ReadyToFlash/Root_Files/BETA-SuperSU-v2.52.zip"

ERROR: ADB Operation timed out

md5sum.exe "C:\Program Files (x86)\WugFresh Development\Nexus Root Toolkit\data\Root_Files\BETA-SuperSU-v2.52.zip"

\1e61d4691e6aa25ae0ea563b0763155b *C:\\Program Files (x86)\\WugFresh Development\\Nexus Root Toolkit\\data\\Root_Files\\BETA-SuperSU-v2.52.zip

Verifying hash of transferred file...

adb shell /sbin/busybox md5sum "/sdcard/!ReadyToFlash/Root_Files/BETA-SuperSU-v2.52.zip"

md5sum: can't open '/sdcard/!ReadyToFlash/Root_Files/BETA-SuperSU-v2.52.zip': No such file or directory

Mismatch. Retrying push (attempt #1 of 2)...

Pushing "BETA-SuperSU-v2.52.zip" to your device...

adb push "C:\Program Files (x86)\WugFresh Development\Nexus Root Toolkit\data\Root_Files\BETA-SuperSU-v2.52.zip" "/sdcard/!ReadyToFlash/Root_Files/BETA-SuperSU-v2.52.zip"

ERROR: ADB Operation timed out

md5sum.exe "C:\Program Files (x86)\WugFresh Development\Nexus Root Toolkit\data\Root_Files\BETA-SuperSU-v2.52.zip"

\1e61d4691e6aa25ae0ea563b0763155b *C:\\Program Files (x86)\\WugFresh Development\\Nexus Root Toolkit\\data\\Root_Files\\BETA-SuperSU-v2.52.zip

Verifying hash of transferred file...

adb shell /sbin/busybox md5sum "/sdcard/!ReadyToFlash/Root_Files/BETA-SuperSU-v2.52.zip"

md5sum: can't open '/sdcard/!ReadyToFlash/Root_Files/BETA-SuperSU-v2.52.zip': No such file or directory

Mismatch. Retrying push (attempt #2 of 2)...

Pushing "BETA-SuperSU-v2.52.zip" to your device...

adb push "C:\Program Files (x86)\WugFresh Development\Nexus Root Toolkit\data\Root_Files\BETA-SuperSU-v2.52.zip" "/sdcard/!ReadyToFlash/Root_Files/BETA-SuperSU-v2.52.zip"

ERROR: ADB Operation timed out

md5sum.exe "C:\Program Files (x86)\WugFresh Development\Nexus Root Toolkit\data\Root_Files\BETA-SuperSU-v2.52.zip"

\1e61d4691e6aa25ae0ea563b0763155b *C:\\Program Files (x86)\\WugFresh Development\\Nexus Root Toolkit\\data\\Root_Files\\BETA-SuperSU-v2.52.zip

Verifying hash of transferred file...

adb shell /sbin/busybox md5sum "/sdcard/!ReadyToFlash/Root_Files/BETA-SuperSU-v2.52.zip"

md5sum: can't open '/sdcard/!ReadyToFlash/Root_Files/BETA-SuperSU-v2.52.zip': No such file or directory

Checking ADB/FASTBOOT Connectivity

adb devices

R32D100SMLT	device

fastboot devices

Connectivity Status: ADB Device Connected

Pushing "BETA-SuperSU-v2.52.zip" to your device...

adb push "C:\Program Files (x86)\WugFresh Development\Nexus Root Toolkit\data\Root_Files\BETA-SuperSU-v2.52.zip" "/sdcard/!ReadyToFlash/Root_Files/BETA-SuperSU-v2.52.zip"

ERROR: ADB Operation timed out

md5sum.exe "C:\Program Files (x86)\WugFresh Development\Nexus Root Toolkit\data\Root_Files\BETA-SuperSU-v2.52.zip"

\1e61d4691e6aa25ae0ea563b0763155b *C:\\Program Files (x86)\\WugFresh Development\\Nexus Root Toolkit\\data\\Root_Files\\BETA-SuperSU-v2.52.zip

Verifying hash of transferred file...

adb shell /sbin/busybox md5sum "/sdcard/!ReadyToFlash/Root_Files/BETA-SuperSU-v2.52.zip"

Mismatch. Retrying push (attempt #1 of 2)...

Pushing "BETA-SuperSU-v2.52.zip" to your device...

adb push "C:\Program Files (x86)\WugFresh Development\Nexus Root Toolkit\data\Root_Files\BETA-SuperSU-v2.52.zip" "/sdcard/!ReadyToFlash/Root_Files/BETA-SuperSU-v2.52.zip"

md5sum.exe "C:\Program Files (x86)\WugFresh Development\Nexus Root Toolkit\data\Root_Files\BETA-SuperSU-v2.52.zip"

\1e61d4691e6aa25ae0ea563b0763155b *C:\\Program Files (x86)\\WugFresh Development\\Nexus Root Toolkit\\data\\Root_Files\\BETA-SuperSU-v2.52.zip

Verifying hash of transferred file...

adb shell /sbin/busybox md5sum "/sdcard/!ReadyToFlash/Root_Files/BETA-SuperSU-v2.52.zip"

Mismatch. Retrying push (attempt #2 of 2)...

Pushing "BETA-SuperSU-v2.52.zip" to your device...

adb push "C:\Program Files (x86)\WugFresh Development\Nexus Root Toolkit\data\Root_Files\BETA-SuperSU-v2.52.zip" "/sdcard/!ReadyToFlash/Root_Files/BETA-SuperSU-v2.52.zip"

md5sum.exe "C:\Program Files (x86)\WugFresh Development\Nexus Root Toolkit\data\Root_Files\BETA-SuperSU-v2.52.zip"

\1e61d4691e6aa25ae0ea563b0763155b *C:\\Program Files (x86)\\WugFresh Development\\Nexus Root Toolkit\\data\\Root_Files\\BETA-SuperSU-v2.52.zip

Verifying hash of transferred file...

adb shell /sbin/busybox md5sum "/sdcard/!ReadyToFlash/Root_Files/BETA-SuperSU-v2.52.zip"

Mimatch. Giving up... Try another USB port and start the process over.""

I have no idea what when wrong, or subsequently right but in the end I manged to restore the last working LMY48X nandroid I had (the one with 0 system memory and somhow It now shows 175M availble and hence allowed me to install Xposed again.

So for now my problem is solved, Im on LMY48X, rooted, TWRP is working fine, XPosed is up and running and I am smiling again.