Yet another corrupted partition table on macOS Mojave

Question

I've seen a couple of posts on here addressing similar issues. Since I don't have in-depth understanding of what went wrong I have to describe what happened in my case and hope you'll help me. Thanks.

MBP 15", Retina, mid 2012. Mojave.

1. I shrank (removed 64Gb) osx space through Disk Utility, installed rEFInd and then Ubuntu 18.04. That worked great. I could boot whatever I chose.
2. Then I decided to shrink osx space a bit more and format the resulting empty space (another 64Gb) to FAT through Disk Utility. After that I booted through a USB drive and tried to install Windows 10 Pro on that new partition.

During the second step, Windows Installer did't like that FAT partition so I erased it (cleaned). It still didn't like it. I deleted it. And re-created the new one from the resulting empty space. It still didn't like it. I decided to quit and leave until tomorrow. Rebooted my machine. Fail. macOS no longer boots and the process gets straight to Ubuntu, from which I'm writing now. I will update this message as soon as I get the required commands outputs.

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-bash-3.2# diskutil list
/dev/disk0
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:      GUID_partition_scheme                        *500.3 GB   disk0
   1:                        EFI                         209.7 MB   disk0s1
   2:          Apple_CoreStorage                         371.5 GB   disk0s2
   3: DE94BBA4-06D1-4D40-A16A-BFD50179D6AC               523.2 MB   disk0s3
   4:                        EFI                         104.9 MB   disk0s4
   5:         Microsoft Reserved                         16.8 MB    disk0s5
   6:       Microsoft Basic Data                         63.9 GB    disk0s6
   7:                 Linux Swap                         4.0 GB     disk0s7
   8: 0FC63DAF-8483-4772-8E79-3D69D8477DE4               60.0 GB    disk0s8
/dev/disk1
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:     Apple_partition_scheme                        *1.2 GB     disk1
   1:        Apple_partition_map                         30.7 KB    disk1s1
   2:                  Apple_HFS Mac OS X Base System    1.2 GB     disk1s2
/dev/disk2
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:                            untitled               *524.3 KB   disk2
/dev/disk3
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:                            untitled               *524.3 KB   disk3
/dev/disk4
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:                            untitled               *524.3 KB   disk4
/dev/disk5
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:                            untitled               *524.3 KB   disk5
/dev/disk6
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:                            untitled               *524.3 KB   disk6
/dev/disk7
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:                            untitled               *6.3 MB     disk7
/dev/disk8
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:                            untitled               *2.1 MB     disk8
/dev/disk9
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:                            untitled               *1.0 MB     disk9
/dev/disk10
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:                            untitled               *524.3 KB   disk10
/dev/disk11
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:                            untitled               *524.3 KB   disk11
/dev/disk12
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:                            untitled               *1.0 MB     disk12
-bash-3.2# gpt -r show disk0
      start       size  index  contents
      0          1         PMBR
      1          1         Pri GPT header
      2         32         Pri GPT table
     34          6

     40     409600      1  GPT part - C12A7328-F81F-11D2-BA4B-00A0C93EC93B
     409640  725609832      2  GPT part - 53746F72-6167-11AA-AA11-00306543ECAC
  726019472        624

  726020096    1021952      3  GPT part - DE94BBA4-06D1-4D40-A16A-BFD50179D6AC
  727042048     204800      4  GPT part - C12A7328-F81F-11D2-BA4B-00A0C93EC93B
  727246848      32768      5  GPT part - E3C9E316-0B5C-4DB8-817D-F92DF00215AE
  727279616  124825600      6  GPT part - EBD0A0A2-B9E5-4433-87C0-68B6B72699C7
  852105216    7813120      7  GPT part - 0657FD6D-A4AB-43C4-84E5-0933C84B4F4F
  859918336  117186560      8  GPT part - 0FC63DAF-8483-4772-8E79-3D69D8477DE4
  977104896        131

  977105027         32         Sec GPT table
  977105059          1         Sec GPT header
-bash-3.2# dd if=/dev/disk0 bs=512 skip=409640 count=1
rY
  +?,C??)?NXSB??g??蝳C??T?"[?L9?
                            9?),lߌ???W9?-d?s?s1+0 records in 1+0 records out 512 bytes transferred in 0.006626 secs (77273 bytes/sec) -

bash-3.2#

Sorry for the last command output, hexdump is not available in my machine's recovery mode. I'm working from crippled terminal.

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EDIT #1: Stil cannot find hexdump or od in recovery mode. However, I've been able to do this:

-bash-3.2# fsck_apfs /dev/disk0s2
Cannot run fsck repair in install environment, degrading fsck_apfs to run with [-n] 
** Checking the container superblock.
** Checking the EFI jumpstart record.
** Checking the space manager.
** Checking the space manager free queue trees.
** Checking the object map.
** Checking volume.
** Checking the APFS volume superblock.
** The volume Macintosh HD was formatted by hfs_convert (748.1.46) and last modified by apfs_kext (945.220.38).
** Checking the object map.
** Checking the snapshot metadata tree.
** Checking the snapshot metadata.
** Checking the extent ref tree.
** Checking the fsroot tree.
error: btn: invalid btn_btree.bt_key_count (expected 12785968, actual 12786023)
Fix btree: bt_key_count (12786023)? NO
   fsroot tree is invalid.
** The volume /dev/disk0s2 could not be verified completely.

Answer 1

If you suspect disk0s2 is is actually a APFS container, then you change the partition type in the GUID Partition Table (GPT) to APFS. Normally one would first hex dump the beginning of disk0s2 to see if the content matches what is expected for a APFS container. Apparently, the is difficult from Recovery mode. A last resort would be to see if the APFS magic number would be the characters NXSB. This can done by entering the commands given below.

dd if=/dev/disk0s2 count=4 skip=32 bs=1 2>/dev/null; echo

If the partition is a APFS container, then the following be output.

NXSB

Note: Any error messages produced by dd command will not be shown. To display these messages omit 2>/dev/null. Doing so on a APFS container partition would produce an output similar to what is shown below.

NXSB4+0 records in
4+0 records out
4 bytes transferred in 0.020234 secs (198 bytes/sec) 

However, if you look at the dd output already posted to your question, you can see the NXSB characters.

If you can boot Ubuntu, then you could hex dump the first sector of the APFS container partition by entering the command given below.

sudo hexdump -Cv -n 512 /dev/sda2

Changing the partition type from Core Storage to APFS

The easiest way to change a partition type is to use the third party gdisk command. This command can be run from Ubuntu already installed on your Mac.

You can make the partition type change form Ubuntu by using the gdisk command. You will need version 1.0.4 of gdisk. If you have an older version then download and install the updated version from the SourceForge GPT fdisk website. The command to enter is given below.

sudo gdisk /dev/sda

Below is an example of the proper interaction with gdisk.

GPT fdisk (gdisk) version 1.0.4

Partition table scan:
  MBR: protective
  BSD: not present
  APM: not present
  GPT: present

Found valid GPT with protective MBR; using GPT.

Command (? for help): t
Partition number (1-8): 2
Current type is 'Apple Core Storage'
Hex code or GUID (L to show codes, Enter = 8300): af0a
Changed type of partition to 'Apple APFS'

Command (? for help): w

Final checks complete. About to write GPT data. THIS WILL OVERWRITE EXISTING
PARTITIONS!!

Do you want to proceed? (Y/N): y
OK; writing new GUID partition table (GPT) to /dev/sda.
Warning: The kernel is still using the old partition table.
The new table will be used at the next reboot or after you
run partprobe(8) or kpartx(8)
The operation has completed successfully.

You can also change the partition type from macOS. The different ways to boot are as follows.

• Boot from an external drive with macOS already installed. Open a Terminal application window to enter the necessary commands.
• Boot to macOS Recovery over the Internet. Once booted over the Internet, you can open a Terminal window to enter the necessary commands.
• Use another Mac to create a USB bootable installer for macOS. Once booted to the installer, you can open a Terminal window to enter the necessary commands.
• Boot the Mac in Target Disk mode and connect to another Mac. In this case, the drive will not be disk0. You will need to run diskutil list to determine the correct identifier.

The commands to enter are shown below.

sudo diskutil unmountdisk disk0
sudo gpt remove -i 2
sudo diskutil unmountdisk disk0
sudo gpt add -i 2 -b 409640 -s 725609832 -t 7C3457EF-0000-11AA-AA11-00306543ECAC /dev/disk0

Note: Most of gpt commands require the drive to be unmounted. Since macOS likes to auto mount partitions, you may need to enter the command diskutil unmountdisk disk0 before entering each gpt command.