Thanks all, I went through the process again and now it's saving the console and other files.
I think the problem may have been in my patience. When installing, I would restart it if there was a really long period of no feedback. I let it work longer this time during all the steps and saw it continue doing more stuff. It might be that I just couldn't expect it to work as fast as I thought.

I found that on my system, it's

cat /sys/class/leds/omega2p\:amber\:system/trigger

And I get this:

root@Omega-B1A3:/sys/class/leds# cat omega2p\:amber\:system/trigger
none [timer] default-on netdev transient mmc0 gpio heartbeat morse oneshot

So, I used this:

echo default-on > /sys/class/leds/omega2p\:amber\:system/trigger

After that, the amber light stays lit... until I turn it off and back on. It blinks continually again and I see that my change didn't stick.

root@Omega-B1A3:~# cat /sys/class/leds/omega2p\:amber\:system/trigger
none [timer] default-on netdev transient mmc0 gpio heartbeat morse oneshot

This seems like a problem with the flash memory...

I should make it clear that what seems like the bigger issue is that nothing stays installed. I added php and added the basic index.php so I could view it. It worked but when I turned it off and back on, I couldn't get it again. It was gone.

@Iker Using the first line you suggested, I get this result:

root@Omega-B1A3:~# cat /sys/class/leds/onion\:amber\:system/trigger
cat: can't open '/sys/class/leds/onion:amber:system/trigger': No such file or directory

Am I misunderstanding what you suggested?

I am having the same issue. The orange led never stops flashing. What did you do to resolve it? What firmware, etc.?

@cusackph You rock. I installed again and it was listed. I did the steps and voila! I'm back in action. Well, I'm back to where I was when the console wouldn't show any apps after restarting. But at least now I can troubleshoot something besides a paperweight.

Thanks a ton!

@cusackph This probably makes me sound like a total n00b but how did you connect the Omega to your USB adapter?
I am guessing you plugged the USB into your computer. Then wires with pins on each end (don't know the official name) to connect the middle two USB adapter wires to the TX and RX holes in your arduino? I don't have the arduino adapter so I'm trying to figure out how to do this with the expansion board. The expansion board has TX+/- and RX+/-.

The output is the same when the dock is unplugged vs plugged in and lights flashing, during the 30 sec it flashes after turning it on with the reset button pressed. I copied the list and diff'd it to make sure. Here's what I get though:

/dev > ls -al tty*
crw-rw-rw-  1 root        wheel    2,   0 Jan 25 11:59 tty
crw-rw-rw-  1 root        wheel   31,   0 Jan 25 12:01 tty.Bluetooth-Incoming-Port
crw-rw-rw-  1 root        wheel   31,   2 Jan 25 12:01 tty.Bluetooth-Modem
crw-rw-rw-  1 root        wheel   31,   4 Jan 25 12:01 tty.MickelsonsiPad-Wireless
crw-rw-rw-  1 root        wheel    4,   0 Jan 25 11:59 ttyp0
crw-rw-rw-  1 root        wheel    4,   1 Jan 25 11:59 ttyp1
crw-rw-rw-  1 root        wheel    4,   2 Jan 25 11:59 ttyp2
crw-rw-rw-  1 root        wheel    4,   3 Jan 25 11:59 ttyp3
crw-rw-rw-  1 root        wheel    4,   4 Jan 25 11:59 ttyp4
crw-rw-rw-  1 root        wheel    4,   5 Jan 25 11:59 ttyp5
crw-rw-rw-  1 root        wheel    4,   6 Jan 25 11:59 ttyp6
crw-rw-rw-  1 root        wheel    4,   7 Jan 25 11:59 ttyp7
crw-rw-rw-  1 root        wheel    4,   8 Jan 25 11:59 ttyp8
crw-rw-rw-  1 root        wheel    4,   9 Jan 25 11:59 ttyp9
crw-rw-rw-  1 root        wheel    4,  10 Jan 25 11:59 ttypa
crw-rw-rw-  1 root        wheel    4,  11 Jan 25 11:59 ttypb
crw-rw-rw-  1 root        wheel    4,  12 Jan 25 11:59 ttypc
crw-rw-rw-  1 root        wheel    4,  13 Jan 25 11:59 ttypd
crw-rw-rw-  1 root        wheel    4,  14 Jan 25 11:59 ttype
crw-rw-rw-  1 root        wheel    4,  15 Jan 25 11:59 ttypf
crw-rw-rw-  1 root        wheel    4,  16 Jan 25 11:59 ttyq0
crw-rw-rw-  1 root        wheel    4,  17 Jan 25 11:59 ttyq1
crw-rw-rw-  1 root        wheel    4,  18 Jan 25 11:59 ttyq2
crw-rw-rw-  1 root        wheel    4,  19 Jan 25 11:59 ttyq3
crw-rw-rw-  1 root        wheel    4,  20 Jan 25 11:59 ttyq4
crw-rw-rw-  1 root        wheel    4,  21 Jan 25 11:59 ttyq5
crw-rw-rw-  1 root        wheel    4,  22 Jan 25 11:59 ttyq6
crw-rw-rw-  1 root        wheel    4,  23 Jan 25 11:59 ttyq7
crw-rw-rw-  1 root        wheel    4,  24 Jan 25 11:59 ttyq8
crw-rw-rw-  1 root        wheel    4,  25 Jan 25 11:59 ttyq9
crw-rw-rw-  1 root        wheel    4,  26 Jan 25 11:59 ttyqa
crw-rw-rw-  1 root        wheel    4,  27 Jan 25 11:59 ttyqb
crw-rw-rw-  1 root        wheel    4,  28 Jan 25 11:59 ttyqc
crw-rw-rw-  1 root        wheel    4,  29 Jan 25 11:59 ttyqd
crw-rw-rw-  1 root        wheel    4,  30 Jan 25 11:59 ttyqe
crw-rw-rw-  1 root        wheel    4,  31 Jan 25 11:59 ttyqf
crw-rw-rw-  1 root        wheel    4,  32 Jan 25 11:59 ttyr0
crw-rw-rw-  1 root        wheel    4,  33 Jan 25 11:59 ttyr1
crw-rw-rw-  1 root        wheel    4,  34 Jan 25 11:59 ttyr2
crw-rw-rw-  1 root        wheel    4,  35 Jan 25 11:59 ttyr3
crw-rw-rw-  1 root        wheel    4,  36 Jan 25 11:59 ttyr4
crw-rw-rw-  1 root        wheel    4,  37 Jan 25 11:59 ttyr5
crw-rw-rw-  1 root        wheel    4,  38 Jan 25 11:59 ttyr6
crw-rw-rw-  1 root        wheel    4,  39 Jan 25 11:59 ttyr7
crw-rw-rw-  1 root        wheel    4,  40 Jan 25 11:59 ttyr8
crw-rw-rw-  1 root        wheel    4,  41 Jan 25 11:59 ttyr9
crw-rw-rw-  1 root        wheel    4,  42 Jan 25 11:59 ttyra
crw-rw-rw-  1 root        wheel    4,  43 Jan 25 11:59 ttyrb
crw-rw-rw-  1 root        wheel    4,  44 Jan 25 11:59 ttyrc
crw-rw-rw-  1 root        wheel    4,  45 Jan 25 11:59 ttyrd
crw-rw-rw-  1 root        wheel    4,  46 Jan 25 11:59 ttyre
crw-rw-rw-  1 root        wheel    4,  47 Jan 25 11:59 ttyrf
crw-rw-rw-  1 root        wheel    4,  48 Jan 25 11:59 ttys0
crw--w----  1 mmickelson  tty     16,   0 Jan 25 12:59 ttys000
crw--w----  1 mmickelson  tty     16,   1 Jan 25 12:57 ttys001
crw--w----  1 mmickelson  tty     16,   2 Jan 25 12:57 ttys002
crw--w----  1 mmickelson  tty     16,   3 Jan 25 12:57 ttys003
crw--w----  1 mmickelson  tty     16,   4 Jan 25 12:57 ttys004
crw--w----  1 mmickelson  tty     16,   5 Jan 25 12:57 ttys005
crw--w----  1 mmickelson  tty     16,   6 Jan 25 12:57 ttys006
crw-rw-rw-  1 root        wheel    4,  49 Jan 25 11:59 ttys1
crw-rw-rw-  1 root        wheel    4,  50 Jan 25 11:59 ttys2
crw-rw-rw-  1 root        wheel    4,  51 Jan 25 11:59 ttys3
crw-rw-rw-  1 root        wheel    4,  52 Jan 25 11:59 ttys4
crw-rw-rw-  1 root        wheel    4,  53 Jan 25 11:59 ttys5
crw-rw-rw-  1 root        wheel    4,  54 Jan 25 11:59 ttys6
crw-rw-rw-  1 root        wheel    4,  55 Jan 25 11:59 ttys7
crw-rw-rw-  1 root        wheel    4,  56 Jan 25 11:59 ttys8
crw-rw-rw-  1 root        wheel    4,  57 Jan 25 11:59 ttys9
crw-rw-rw-  1 root        wheel    4,  58 Jan 25 11:59 ttysa
crw-rw-rw-  1 root        wheel    4,  59 Jan 25 11:59 ttysb
crw-rw-rw-  1 root        wheel    4,  60 Jan 25 11:59 ttysc
crw-rw-rw-  1 root        wheel    4,  61 Jan 25 11:59 ttysd
crw-rw-rw-  1 root        wheel    4,  62 Jan 25 11:59 ttyse
crw-rw-rw-  1 root        wheel    4,  63 Jan 25 11:59 ttysf
crw-rw-rw-  1 root        wheel    4,  64 Jan 25 11:59 ttyt0
crw-rw-rw-  1 root        wheel    4,  65 Jan 25 11:59 ttyt1
crw-rw-rw-  1 root        wheel    4,  66 Jan 25 11:59 ttyt2
crw-rw-rw-  1 root        wheel    4,  67 Jan 25 11:59 ttyt3
crw-rw-rw-  1 root        wheel    4,  68 Jan 25 11:59 ttyt4
crw-rw-rw-  1 root        wheel    4,  69 Jan 25 11:59 ttyt5
crw-rw-rw-  1 root        wheel    4,  70 Jan 25 11:59 ttyt6
crw-rw-rw-  1 root        wheel    4,  71 Jan 25 11:59 ttyt7
crw-rw-rw-  1 root        wheel    4,  72 Jan 25 11:59 ttyt8
crw-rw-rw-  1 root        wheel    4,  73 Jan 25 11:59 ttyt9
crw-rw-rw-  1 root        wheel    4,  74 Jan 25 11:59 ttyta
crw-rw-rw-  1 root        wheel    4,  75 Jan 25 11:59 ttytb
crw-rw-rw-  1 root        wheel    4,  76 Jan 25 11:59 ttytc
crw-rw-rw-  1 root        wheel    4,  77 Jan 25 11:59 ttytd
crw-rw-rw-  1 root        wheel    4,  78 Jan 25 11:59 ttyte
crw-rw-rw-  1 root        wheel    4,  79 Jan 25 11:59 ttytf
crw-rw-rw-  1 root        wheel    4,  80 Jan 25 11:59 ttyu0
crw-rw-rw-  1 root        wheel    4,  81 Jan 25 11:59 ttyu1
crw-rw-rw-  1 root        wheel    4,  82 Jan 25 11:59 ttyu2
crw-rw-rw-  1 root        wheel    4,  83 Jan 25 11:59 ttyu3
crw-rw-rw-  1 root        wheel    4,  84 Jan 25 11:59 ttyu4
crw-rw-rw-  1 root        wheel    4,  85 Jan 25 11:59 ttyu5
crw-rw-rw-  1 root        wheel    4,  86 Jan 25 11:59 ttyu6
crw-rw-rw-  1 root        wheel    4,  87 Jan 25 11:59 ttyu7
crw-rw-rw-  1 root        wheel    4,  88 Jan 25 11:59 ttyu8
crw-rw-rw-  1 root        wheel    4,  89 Jan 25 11:59 ttyu9
crw-rw-rw-  1 root        wheel    4,  90 Jan 25 11:59 ttyua
crw-rw-rw-  1 root        wheel    4,  91 Jan 25 11:59 ttyub
crw-rw-rw-  1 root        wheel    4,  92 Jan 25 11:59 ttyuc
crw-rw-rw-  1 root        wheel    4,  93 Jan 25 11:59 ttyud
crw-rw-rw-  1 root        wheel    4,  94 Jan 25 11:59 ttyue
crw-rw-rw-  1 root        wheel    4,  95 Jan 25 11:59 ttyuf
crw-rw-rw-  1 root        wheel    4,  96 Jan 25 11:59 ttyv0
crw-rw-rw-  1 root        wheel    4,  97 Jan 25 11:59 ttyv1
crw-rw-rw-  1 root        wheel    4,  98 Jan 25 11:59 ttyv2
crw-rw-rw-  1 root        wheel    4,  99 Jan 25 11:59 ttyv3
crw-rw-rw-  1 root        wheel    4, 100 Jan 25 11:59 ttyv4
crw-rw-rw-  1 root        wheel    4, 101 Jan 25 11:59 ttyv5
crw-rw-rw-  1 root        wheel    4, 102 Jan 25 11:59 ttyv6
crw-rw-rw-  1 root        wheel    4, 103 Jan 25 11:59 ttyv7
crw-rw-rw-  1 root        wheel    4, 104 Jan 25 11:59 ttyv8
crw-rw-rw-  1 root        wheel    4, 105 Jan 25 11:59 ttyv9
crw-rw-rw-  1 root        wheel    4, 106 Jan 25 11:59 ttyva
crw-rw-rw-  1 root        wheel    4, 107 Jan 25 11:59 ttyvb
crw-rw-rw-  1 root        wheel    4, 108 Jan 25 11:59 ttyvc
crw-rw-rw-  1 root        wheel    4, 109 Jan 25 11:59 ttyvd
crw-rw-rw-  1 root        wheel    4, 110 Jan 25 11:59 ttyve
crw-rw-rw-  1 root        wheel    4, 111 Jan 25 11:59 ttyvf
crw-rw-rw-  1 root        wheel    4, 112 Jan 25 11:59 ttyw0
crw-rw-rw-  1 root        wheel    4, 113 Jan 25 11:59 ttyw1
crw-rw-rw-  1 root        wheel    4, 114 Jan 25 11:59 ttyw2
crw-rw-rw-  1 root        wheel    4, 115 Jan 25 11:59 ttyw3
crw-rw-rw-  1 root        wheel    4, 116 Jan 25 11:59 ttyw4
crw-rw-rw-  1 root        wheel    4, 117 Jan 25 11:59 ttyw5
crw-rw-rw-  1 root        wheel    4, 118 Jan 25 11:59 ttyw6
crw-rw-rw-  1 root        wheel    4, 119 Jan 25 11:59 ttyw7
crw-rw-rw-  1 root        wheel    4, 120 Jan 25 11:59 ttyw8
crw-rw-rw-  1 root        wheel    4, 121 Jan 25 11:59 ttyw9
crw-rw-rw-  1 root        wheel    4, 122 Jan 25 11:59 ttywa
crw-rw-rw-  1 root        wheel    4, 123 Jan 25 11:59 ttywb
crw-rw-rw-  1 root        wheel    4, 124 Jan 25 11:59 ttywc
crw-rw-rw-  1 root        wheel    4, 125 Jan 25 11:59 ttywd
crw-rw-rw-  1 root        wheel    4, 126 Jan 25 11:59 ttywe
crw-rw-rw-  1 root        wheel    4, 127 Jan 25 11:59 ttywf

@cusackph When I use ls /dev/tty* and I get a lot more items (expected).
I'm using the expansion dock, powered from the USB cable attached to my computer.
I restarted but still no luck.

Well done documenting your steps in the un-bricking adventure. I've ordered the USB adapter and will push forward when it arrives.

I installled the driver linked to from https://docs.onion.io/omega2-docs/connecting-to-the-omega-terminal.html#connecting-via-serial-mac, but the device never showed up when using ls tty.*. Either the driver didn't install correctly or my Omega2+ is really dead.