Configure MongoDB on Monkey Island initialization

[mssalvatore]

Monkey Island needs to write runtime artifacts to a writable location and assume that the source code directory is read-only. Currently, MongoDB is started by the linux/run.sh, windows\run_mongodb.bat, and appimage/run_appimage.sh. These scripts do not have access to the data_dir property in server_config.json, and giving them access would add even more redundant functionality to all of these scripts.

• Add a "mongodb" section to the server_config.json with a "start_mongodb" boolean. (0) - @VakarisZ

{
    "log_level": "debug",
    "data_dir": "$HOME/.monkey_island",
    "environment": {
        "server_config": "password",
        "deployment": "development",
        "user": "my_user",
        "password_hash": "DEADBEEF"
    }
    "mongodb" {
        "start_mongodb": true
    }
}

• Make sure this section exists and is correct for the default server_config.json, the docker server_config.json, the windows installer server_config.json, and the AppImage server_config.json

• If "start_mongodb": true, then monkey_island.py will start the mongodb process and set it's --dbpath argument to data_dir/db. (0d) - @VakarisZ

• Refactor the data dir folder creation and permission setting into a separate function and re-use it to create db dir with relevant permissions as well (0d).

• Refactor mongodb initialization to be decoupled from environment config (0d) - @VakarisZ

• Remove the code that starts mongodb from appimage/run_appimage.sh. If this script no longer serves any purpose, remove it and modify the AppImage to run without it. (0d) - @VakarisZ

• Remove linux/run.sh. Modify documentation with new instructions on how to start monkey island. (0d) - @VakarisZ

• Remove code that creates db dir from deployment scripts, mongodb install scripts, docs, etc. (0) - @VakarisZ

• Remove the code that starts mongodb from monkey_island/windows/*. If any of these scripts no longer serves a purpose, remove them.(0d) - @VakarisZ

• Ensure the mongodb process is properly cleaned up when Monkey Island exits (0d)

• Review PR and fix (0d)