I was able to run the server from PyCharm and connect to the web interface!

I'm up and running!

You can start with this values. 

"serial": {
    "plattform_type": "ciclop",
    "baudrate": 14400,
    "autoflash": "True",
    "port": "/dev/ttyUSB0",
    "flash_baudrate": 115200
}

Otherwise we need to find some fitting settings. You can do a quick connection test with this command: 

sudo avrdude-autoreset -p m328p -b 115200 -carduino -P/dev/ttyUSB0

This command should list some information about the microcontroller on the arduino. If you are getting errors instead you need to find the error. Possible reasons are a wrong baudrate... try 57600, 38400, 14400 instead. But also the device might be wrong, you can try /dev/ttyUSB1 also.

When you are getting a nice output you can try to run it again with pycharm.

ssh://pi@10.25.25.145:22/usr/bin/python3 -u /home/pi/dev/FabScanPi-Server/src/fabscanpi-server --loglevel=debug --config=/home/pi/dev/FabScanPi-Server/src/fabscan/config/dev.config.json --settings=/home/pi/dev/FabScanPi-Server/src/fabscan/config/default.settings.json
avrdude-original: Using autoreset DTR on GPIO Pin 7
sudo: /usr/bin/avrdude: command not found
2020-06-14 18:12:36,766  INFO - fabscan.server.FSScanServer: FabScanPi-Server 0.9.1
2020-06-14 18:12:36,769  DEBUG - fabscan.scanner.interfaces: Scanner Type is: laserscanner
2020-06-14 18:12:37,658  DEBUG - fabscan.scanner.laserscanner.driver.FSSerial: Port in Config found
2020-06-14 18:12:37,660  DEBUG - fabscan.scanner.laserscanner.driver.FSSerial: Latest available firmware version is: v.20200306
2020-06-14 18:12:37,778  ERROR - fabscan.scanner.laserscanner.driver.FSSerial: Communication error on port /dev/ttyUSB0 try other flashing baudrate than 115200. Maybe corrupted bootloader.
2020-06-14 18:12:37,779  ERROR - fabscan.scanner.laserscanner.driver.FSSerial: Fatal FabScanPi HAT or compatible connection error....'NoneType' object has no attribute 'isOpen'
2020-06-14 18:12:37,779  INFO - fabscan.server.FSScanServer: FabScan Server Exit. Bye!

Process finished with exit code 0

The username is pi and password raspberry. IP Adress is of course the address of your pi. Afterwards you need to select this new added python interpreter as default in your run configuration.

/usr/bin/python3.8 /snap/pycharm-professional/201/plugins/python/helpers/pydev/pydevd.py --multiproc --qt-support=auto --client 127.0.0.1 --port 41111 --file /home/mping/dev/FabScanPi-Server/src/fabscanpi-server --loglevel=debug --config=/home/pi/fabscan/src/fabscan/config/dev.config.json --settings=/home/pi/fabscan/src/fabscan/config/default.settings.json
pydev debugger: process 2318 is connecting

Connected to pydev debugger (build 201.7846.77)
sh: 1: /usr/bin/avrdude-autoreset: not found
2020-06-14 09:09:01,385  INFO - fabscan.server.FSScanServer: FabScanPi-Server 0.9.1
2020-06-14 09:09:01,386  CRITICAL - fabscan: Fatal error:  No such file or directory: '/home/pi/fabscan/src/fabscan/config/dev.config.json'

Process finished with exit code 1

avdrude-autoreset should be contained in the image. You can test it by running it when you are logged in. 

/usr/bin/avrdude-autoreset

Anyway, the file is also part of the FabScanPi Server Package. It is located here:

https://github.com/mariolukas/FabScanPi-Server/tree/develop/src/avrdude

The package installer copies it to /usr/bin and makes it executable with 

chmod a+x /usr/bin/avrdude-autoreset

https://github.com/mharizanov/avrdude-rpi

/usr/bin/python3.8 /home/mping/dev/FabScanPi-Server/src/fabscanpi-server --loglevel=debug --config=/home/pi/fabscan/src/fabscan/config/dev.config.json --settings=/home/pi/fabscan/src/fabscan/config/default.settings.json
sh: 1: /usr/bin/avrdude-autoreset: not found
2020-06-12 17:18:23,886  INFO - fabscan.server.FSScanServer: FabScanPi-Server 0.9.1
2020-06-12 17:18:23,886  CRITICAL - fabscan: Fatal error:  No such file or directory: '/home/pi/fabscan/src/fabscan/config/dev.config.json'

Not sure if I need to install avrdude-autoreset, or where to find it (I see the project on github).

Also not sure if I need to change the remote folder: /home/pi/fabscan/src/fabscan/config/ or if that should be deploying.  Otherwise as far as I can tell my settings match the dev setup directions. 

I did some fiddling with the config settings and got the 0.9.0 running, but still no success from PyCharm

Yes sure. I forgot to add this to the docs. You need to create the FSVersion.py file manually in the folder you linked to the deployment process. The content should be something like: 

__version__="0.9.1"

The Version File is normally created while the Release build process. I think this error should be catched in dev mode. We can set a static dev version number while developing. A simple import check in try catch block should do the job.