I did sudo apt-get install machinekit. Now I get a bunch of new messages.
I am trying to figure out if I somehow screwed up my configs in the process 
of updating machinekit. Here is a link to my .ini file 
<https://pastebin.com/U9n4cKKL>. Here is a link to my .hal file 
<https://pastebin.com/B7QKCu77>.
I have also attached a screen capture of the error/warning message that 
appeared on the axis screen.

cat /var/log/linuxcnc.log gives:
Feb 26 01:18:01 beaglebone msgd:0: startup pid=2670 flavor=rt-preempt 
rtlevel=1 usrlevel=1 halsize=524288 shm=Posix cc=gcc 6.3.0 20170516  
version=v0.1~-----~01fe624
Feb 26 01:18:01 beaglebone msgd:0: ØMQ=4.2.1 czmq=4.0.2 protobuf=3.0.0 
atomics=gcc intrinsics    libwebsockets=2.0.3
Feb 26 01:18:01 beaglebone msgd:0: configured: sha=01fe624
Feb 26 01:18:01 beaglebone msgd:0: built:      Feb 25 2019 07:42:47 
sha=01fe624
Feb 26 01:18:01 beaglebone msgd:0: register_stuff: actual hostname as 
announced by avahi='beaglebone.local'
Feb 26 01:18:01 beaglebone msgd:0: zeroconf: registering: 'Log service on 
beaglebone.local pid 2670'
Feb 26 01:18:02 beaglebone msgd:0: zeroconf: registered 'Log service on 
beaglebone.local pid 2670' _machinekit._tcp 0 TXT 
"uuid=471405b7-f524-4f2a-9697-6061a9855992" 
"instance=5c216bac-3964-11e9-9408-7c669d58a259" "service=log" 
"dsn=ipc:///tmp/0.log.471405b7-f524-4f2a-9697-6061a9855992"
Feb 26 01:18:03 beaglebone msgd:0: hal_lib:2675:rt memmapped gpio port 2 to 
0xb6fb1000, oe: 0xb6fb1134, set: 0xb6fb1194, clr: 0xb6fb1190
Feb 26 01:18:03 beaglebone msgd:0: hal_lib:2675:rt pin 9 maps to pin 2-5, 
mode 85
Feb 26 01:18:03 beaglebone msgd:0: hal_lib:2675:rt pin 10 maps to pin 2-4, 
mode 85
Feb 26 01:18:03 beaglebone msgd:0: hal_lib:2675:rt memmapped gpio port 0 to 
0xb6faf000, oe: 0xb6faf134, set: 0xb6faf194, clr: 0xb6faf190
Feb 26 01:18:03 beaglebone msgd:0: hal_lib:2675:rt pin 14 maps to pin 0-26, 
mode 85
Feb 26 01:18:03 beaglebone msgd:0: hal_lib:2675:rt pin 18 maps to pin 2-1, 
mode 85
Feb 26 01:18:03 beaglebone msgd:0: hal_lib:2675:rt memmapped gpio port 1 to 
0xb6fad000, oe: 0xb6fad134, set: 0xb6fad194, clr: 0xb6fad190
Feb 26 01:18:03 beaglebone msgd:0: hal_lib:2675:rt hpg_stepgen_init
Feb 26 01:18:09 beaglebone rtapi:0: unload: '' not loaded
Feb 26 01:18:09 beaglebone rtapi:0: unload: '' not loaded
Feb 26 01:18:09 beaglebone rtapi:0: unload: '' not loaded
Feb 26 01:18:09 beaglebone rtapi:0: unload: '' not loaded
Feb 26 01:18:09 beaglebone rtapi:0: unload: '' not loaded
Feb 26 01:18:09 beaglebone rtapi:0: unload: '' not loaded
Feb 26 01:18:09 beaglebone rtapi:0: unload: '' not loaded
Feb 26 01:18:09 beaglebone msgd:0: rtapi_app exit detected - scheduled 
shutdown
Feb 26 01:18:11 beaglebone msgd:0: msgd shutting down
Feb 26 01:18:11 beaglebone msgd:0: zeroconf: unregistering 'Log service on 
beaglebone.local pid 2670'
Feb 26 01:18:11 beaglebone msgd:0: log buffer hwm: 0% (8 msgs, 699 bytes 
out of 524288)
Feb 26 01:18:11 beaglebone msgd:0: normal shutdown - global segment detached

machinekit@beaglebone:~$ cat linuxcnc_debug.txt
2648
  PID TTY      STAT   TIME COMMAND
Stopping realtime threads
Unloading hal components

machinekit@beaglebone:~$ cat linuxcnc_print.txt
RUN_IN_PLACE=no
LINUXCNC_DIR=
LINUXCNC_BIN_DIR=/usr/bin
LINUXCNC_TCL_DIR=/usr/lib/tcltk/linuxcnc
LINUXCNC_SCRIPT_DIR=
LINUXCNC_RTLIB_DIR=/usr/lib/linuxcnc
LINUXCNC_CONFIG_DIR=
LINUXCNC_LANG_DIR=/usr/share/linuxcnc/tcl/msgs
INIVAR=/usr/libexec/linuxcnc/inivar
HALCMD=halcmd
LINUXCNC_EMCSH=/usr/bin/wish8.6
INIFILE=/home/machinekit/machinekit/configs/ARM.BeagleBone.Xylotex/Xylotex.ini
PARAMETER_FILE=pru-stepper.var
TASK=milltask
HALUI=halui
DISPLAY=axis
Starting Machinekit server program: linuxcncsvr
Loading Real Time OS, RTAPI, and HAL_LIB modules
Starting Machinekit IO program: io
Starting HAL User Interface program: halui
Killing task linuxcncsvr, PID=2648
Removing HAL_LIB, RTAPI, and Real Time OS modules
Removing NML shared memory segments

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