diff --git a/.setup/CONFIGURE_SUBMITTY.py b/.setup/CONFIGURE_SUBMITTY.py
index f39ff38d631..f2b5cf53bad 100644
--- a/.setup/CONFIGURE_SUBMITTY.py
+++ b/.setup/CONFIGURE_SUBMITTY.py
@@ -2,39 +2,14 @@
 
 import argparse
 from collections import OrderedDict
-import grp
 import json
 import os
-import pwd
 import secrets
 import shutil
 import string
 import tzlocal
-import tempfile
-
-
-def get_uid(user):
-    return pwd.getpwnam(user).pw_uid
-
-
-def get_gid(user):
-    return pwd.getpwnam(user).pw_gid
-
-
-def get_ids(user):
-    try:
-        return get_uid(user), get_gid(user)
-    except KeyError:
-        raise SystemExit("ERROR: Could not find user: " + user)
-
-
-def get_input(question, default=""):
-    add = "[{}] ".format(default) if default != "" else ""
-    user = input("{}: {}".format(question, add)).strip()
-    if user == "":
-        user = default
-    return user
 
+from GENERATE_CONFIGS import generate_config
 
 class StrToBoolAction(argparse.Action):
     """
@@ -56,6 +31,77 @@ def __call__(self, parser, namespace, values, option_string=None):
 if os.getuid() != 0:
     raise SystemExit('ERROR: This script must be run by root or sudo')
 
+authentication_methods = [
+    'PamAuthentication',
+    'DatabaseAuthentication',
+    'LdapAuthentication',
+    'SamlAuthentication'
+]
+
+defaults = {
+    'database_host': 'localhost',
+    'database_port': 5432,
+    'database_user': 'submitty_dbuser',
+    'database_course_user': 'submitty_course_dbuser',
+    'submission_url': '',
+    'supervisor_user': 'submitty',
+    'vcs_url': '',
+    'authentication_method': 0,
+    'institution_name' : '',
+    'institution_homepage' : '',
+    'user_create_account' : False,
+    'timezone' : str(tzlocal.get_localzone()),
+    'submitty_admin_username': '',
+    'email_user': '',
+    'email_password': '',
+    'email_sender': 'submitty@myuniversity.edu',
+    'email_reply_to': 'submitty_do_not_reply@myuniversity.edu',
+    'email_server_hostname': 'mail.myuniversity.edu',
+    'email_server_port': 25,
+    'email_internal_domain': 'example.com',
+    'course_code_requirements': "Please follow your school's convention for course code.",
+    'sys_admin_email': '',
+    'sys_admin_url': '',
+    'ldap_options': {
+        'url': '',
+        'uid': '',
+        'bind_dn': ''
+    },
+    'saml_options': {
+        'name': '',
+        'username_attribute': ''
+    },
+    'course_material_file_upload_limit_mb': 100,
+    'user_id_requirements': {
+        'any_user_id': True,
+        'require_name': False,
+        'min_length': 6,
+        'max_length': 25,
+        # Example for Alyssa Hacker : hackal -- Allows for shorter names. If they are shorter, then it will just take the entire name. 
+        # Example for Joseph Wo : wojo
+        'name_requirements': {
+            'given_first': False,
+            'given_name': 2,
+            'family_name': 4
+        },
+        'require_email': False,
+        # If the user_id must contain part of the email. If whole_email is true, it must match the email.
+        # If whole_prefix is true, then the user_id must equal everything before the final @ sign.
+        # Else, it must be a certain number of characters of the prefix. 
+        # Examples for myemail@email.com:
+        # Whole email: myemail@gmail.com
+        # Whole prefix: myemail
+        # Part of prefix: myemai
+        'email_requirements': {
+            'whole_email': False,
+            'whole_prefix': False,
+            'prefix_count': 6
+        },
+        'accepted_emails': [
+            'gmail.com'
+        ]
+    }
+}
 
 parser = argparse.ArgumentParser(description='Submitty configuration script',
                                  formatter_class=argparse.ArgumentDefaultsHelpFormatter)
@@ -100,51 +146,7 @@ def __call__(self, parser, namespace, values, option_string=None):
 CGI_USER = 'submitty_cgi'
 DAEMON_USER = 'submitty_daemon'
 DAEMON_GROUP = 'submitty_daemon'
-
-if not args.worker:
-    PHP_UID, PHP_GID = get_ids(PHP_USER)
-    CGI_UID, CGI_GID = get_ids(CGI_USER)
-    # System Groups
-    DAEMONPHP_GROUP = 'submitty_daemonphp'
-    try:
-        grp.getgrnam(DAEMONPHP_GROUP)
-    except KeyError:
-        raise SystemExit("ERROR: Could not find group: " + DAEMONPHP_GROUP)
-    DAEMONCGI_GROUP = 'submitty_daemoncgi'
-    try:
-        grp.getgrnam(DAEMONCGI_GROUP)
-    except KeyError:
-        raise SystemExit("ERROR: Could not find group: " + DAEMONCGI_GROUP)
-    DAEMONPHPCGI_GROUP = 'submitty_daemonphpcgi'
-    try:
-        grp.getgrnam(DAEMONPHPCGI_GROUP)
-    except KeyError:
-        raise SystemExit("ERROR: Could not find group: " + DAEMONPHPCGI_GROUP)
-
-DAEMON_UID, DAEMON_GID = get_ids(DAEMON_USER)
-
 COURSE_BUILDERS_GROUP = 'submitty_course_builders'
-try:
-    grp.getgrnam(COURSE_BUILDERS_GROUP)
-except KeyError:
-    raise SystemExit("ERROR: Could not find group: " + COURSE_BUILDERS_GROUP)
-
-##############################################################################
-
-# This is the upper limit of the number of parallel grading threads on
-# this machine
-NUM_UNTRUSTED = 60
-
-FIRST_UNTRUSTED_UID, FIRST_UNTRUSTED_GID = get_ids('untrusted00')
-
-# confirm that the uid/gid of the untrusted users are sequential
-for i in range(1, NUM_UNTRUSTED):
-    untrusted_user = "untrusted{:0=2d}".format(i)
-    uid, gid = get_ids(untrusted_user)
-    if uid != FIRST_UNTRUSTED_UID + i:
-        raise SystemExit('CONFIGURATION ERROR: untrusted UID not sequential: ' + untrusted_user)
-    elif gid != FIRST_UNTRUSTED_GID + i:
-        raise SystemExit('CONFIGURATION ERROR: untrusted GID not sequential: ' + untrusted_user)
 
 ##############################################################################
 
@@ -161,54 +163,24 @@ def __call__(self, parser, namespace, values, option_string=None):
 CONFIGURATION_JSON = os.path.join(SETUP_INSTALL_DIR, 'submitty_conf.json')
 SITE_CONFIG_DIR = os.path.join(SUBMITTY_INSTALL_DIR, "site", "config")
 CONFIG_INSTALL_DIR = os.path.join(SUBMITTY_INSTALL_DIR, 'config')
+SUBMITTY_USERS_JSON = os.path.join(CONFIG_INSTALL_DIR, 'submitty_users.json')
 SUBMITTY_ADMIN_JSON = os.path.join(CONFIG_INSTALL_DIR, 'submitty_admin.json')
 EMAIL_JSON = os.path.join(CONFIG_INSTALL_DIR, 'email.json')
 AUTHENTICATION_JSON = os.path.join(CONFIG_INSTALL_DIR, 'authentication.json')
 
 ##############################################################################
 
-authentication_methods = [
-    'PamAuthentication',
-    'DatabaseAuthentication',
-    'LdapAuthentication',
-    'SamlAuthentication'
-]
-
-defaults = {
-    'database_host': 'localhost',
-    'database_port': 5432,
-    'database_user': 'submitty_dbuser',
-    'database_course_user': 'submitty_course_dbuser',
-    'submission_url': '',
-    'supervisor_user': 'submitty',
-    'vcs_url': '',
-    'authentication_method': 0,
-    'institution_name' : '',
-    'institution_homepage' : '',
-    'user_create_account' : False,
-    'timezone' : str(tzlocal.get_localzone()),
-    'submitty_admin_username': '',
-    'email_user': '',
-    'email_password': '',
-    'email_sender': 'submitty@myuniversity.edu',
-    'email_reply_to': 'submitty_do_not_reply@myuniversity.edu',
-    'email_server_hostname': 'mail.myuniversity.edu',
-    'email_server_port': 25,
-    'email_internal_domain': 'example.com',
-    'course_code_requirements': "Please follow your school's convention for course code.",
-    'sys_admin_email': '',
-    'sys_admin_url': '',
-    'ldap_options': {
-        'url': '',
-        'uid': '',
-        'bind_dn': ''
-    },
-    'saml_options': {
-        'name': '',
-        'username_attribute': ''
-    },
-    'course_material_file_upload_limit_mb': 100
-}
+if os.path.isdir(CONFIG_INSTALL_DIR):
+    for file in os.scandir(CONFIG_INSTALL_DIR):
+        if file.name not in IGNORED_FILES_AND_DIRS:
+            if file.is_file():
+                os.remove(os.path.join(CONFIG_INSTALL_DIR, file.name))
+            else:
+                os.rmdir(os.path.join(CONFIG_INSTALL_DIR, file.name))
+elif os.path.exists(CONFIG_INSTALL_DIR):
+    os.remove(CONFIG_INSTALL_DIR)
+os.makedirs(CONFIG_INSTALL_DIR, exist_ok=True)
+os.chmod(CONFIG_INSTALL_DIR, 0o755)
 
 loaded_defaults = {}
 if os.path.isfile(CONFIGURATION_JSON):
@@ -247,152 +219,7 @@ def __call__(self, parser, namespace, values, option_string=None):
 if args.worker:
     print("CONFIGURING SUBMITTY AS A WORKER !!")
 
-print('Hit enter to use default in []')
-print()
-
-if args.worker:
-    SUPERVISOR_USER = get_input('What is the id for your submitty user?', defaults['supervisor_user'])
-    print('SUPERVISOR USER : {}'.format(SUPERVISOR_USER))
-else:
-    DATABASE_HOST = get_input('What is the database host?', defaults['database_host'])
-    print()
-
-    if not os.path.isdir(DATABASE_HOST):
-        DATABASE_PORT = int(get_input('What is the database port?', defaults['database_port']))
-        print()
-    else:
-        DATABASE_PORT = defaults['database_port']
-
-    DATABASE_USER = get_input('What is the global database user/role?', defaults['database_user'])
-    print()
-
-    default = ''
-    if 'database_password' in defaults and DATABASE_USER == defaults['database_user']:
-        default = '(Leave blank to use same password)'
-    DATABASE_PASS = get_input('What is the password for the global database user/role {}? {}'.format(DATABASE_USER, default))
-    if DATABASE_PASS == '' and DATABASE_USER == defaults['database_user'] and 'database_password' in defaults:
-        DATABASE_PASS = defaults['database_password']
-    print()
-
-    DATABASE_COURSE_USER = get_input('What is the course database user/role?', defaults['database_course_user'])
-    print()
-
-    default = ''
-    if 'database_course_password' in defaults and DATABASE_COURSE_USER == defaults['database_course_user']:
-        default = '(Leave blank to use same password)'
-    DATABASE_COURSE_PASSWORD = get_input('What is the password for the course database user/role {}? {}'.format(DATABASE_COURSE_USER, default))
-    if DATABASE_COURSE_PASSWORD == '' and DATABASE_COURSE_USER == defaults['database_course_user'] and 'database_course_password' in defaults:
-        DATABASE_COURSE_PASSWORD = defaults['database_course_password']
-    print()
-
-    TIMEZONE = get_input('What timezone should Submitty use? (for a full list of supported timezones see http://php.net/manual/en/timezones.php)', defaults['timezone'])
-    print()
-
-    DEFAULT_LOCALE = get_input('What default language should the Submitty site use?', 'en_US')
-    print()
-
-    COURSE_MATERIAL_UPLOAD_LIMIT_MB = get_input('What is the maximum file upload size for course materials (in MB)?', defaults['course_material_file_upload_limit_mb'])
-    print()
-
-    SUBMISSION_URL = get_input('What is the url for submission? (ex: http://192.168.56.101 or '
-                               'https://submitty.cs.rpi.edu)', defaults['submission_url']).rstrip('/')
-    print()
-
-    VCS_URL = get_input('What is the url for VCS? (Leave blank to default to submission url + {$vcs_type}) (ex: http://192.168.56.101/{$vcs_type} or https://submitty-vcs.cs.rpi.edu/{$vcs_type}', defaults['vcs_url']).rstrip('/')
-    print()
-
-    INSTITUTION_NAME = get_input('What is the name of your institution? (Leave blank/type "none" if not desired)',
-                             defaults['institution_name'])
-    print()
-
-    if INSTITUTION_NAME == '' or INSTITUTION_NAME.isspace():
-        INSTITUTION_HOMEPAGE = ''
-    else:
-        INSTITUTION_HOMEPAGE = get_input("What is the url of your institution\'s homepage? "
-                                     '(Leave blank/type "none" if not desired)', defaults['institution_homepage'])
-        if INSTITUTION_HOMEPAGE.lower() == "none":
-            INSTITUTION_HOMEPAGE = ''
-        print()
-    
-    SYS_ADMIN_EMAIL = get_input("What is the email for system administration?", defaults['sys_admin_email'])
-    SYS_ADMIN_URL = get_input("Where to report problems with Submitty (url for help link)?", defaults['sys_admin_url'])
-
-    print('What authentication method to use:')
-    for i in range(len(authentication_methods)):
-        print(f"{i + 1}. {authentication_methods[i]}")
-
-    while True:
-        try:
-            auth = int(get_input('Enter number?', defaults['authentication_method'])) - 1
-        except ValueError:
-            auth = -1
-        if auth in range(len(authentication_methods)):
-            break
-        print(f'Number must in between 1 - {len(authentication_methods)} (inclusive)!')
-    print()
-
-    AUTHENTICATION_METHOD = authentication_methods[auth]
-
-    default_auth_options = defaults.get('ldap_options', dict())
-    LDAP_OPTIONS = {
-        'url': default_auth_options.get('url', ''),
-        'uid': default_auth_options.get('uid', ''),
-        'bind_dn': default_auth_options.get('bind_dn', '')
-    }
-    USER_CREATE_ACCOUNT = False
-    if AUTHENTICATION_METHOD == 'DatabaseAuthentication':
-        user_create_account = get_input("Allow users to create their own accounts? [y/n]", 'n')
-        USER_CREATE_ACCOUNT = user_create_account.lower() in ['yes', 'y']
-        print()
-    if AUTHENTICATION_METHOD == 'LdapAuthentication':
-        LDAP_OPTIONS['url'] = get_input('Enter LDAP url?', LDAP_OPTIONS['url'])
-        LDAP_OPTIONS['uid'] = get_input('Enter LDAP UID?', LDAP_OPTIONS['uid'])
-        LDAP_OPTIONS['bind_dn'] = get_input('Enter LDAP bind_dn?', LDAP_OPTIONS['bind_dn'])
-
-    default_auth_options = defaults.get('saml_options', dict())
-    SAML_OPTIONS = {
-        'name': default_auth_options.get('name', ''),
-        'username_attribute': default_auth_options.get('username_attribute', '')
-    }
-
-    if AUTHENTICATION_METHOD == 'SamlAuthentication':
-        SAML_OPTIONS['name'] = get_input('Enter name you would like shown to user for authentication?', SAML_OPTIONS['name'])
-        SAML_OPTIONS['username_attribute'] = get_input('Enter SAML username attribute?', SAML_OPTIONS['username_attribute'])
-
-
-    CGI_URL = SUBMISSION_URL + '/cgi-bin'
-
-    SUBMITTY_ADMIN_USERNAME = get_input("What is the submitty admin username (optional)?", defaults['submitty_admin_username'])
-
-    while True:
-        is_email_enabled = get_input("Will Submitty use email notifications? [y/n]", 'y')
-        if (is_email_enabled.lower() in ['yes', 'y']):
-            EMAIL_ENABLED = True
-            EMAIL_USER = get_input("What is the email user?", defaults['email_user'])
-            EMAIL_PASSWORD = get_input("What is the email password",defaults['email_password'])
-            EMAIL_SENDER = get_input("What is the email sender address (the address that will appear in the From: line)?",defaults['email_sender'])
-            EMAIL_REPLY_TO = get_input("What is the email reply to address?", defaults['email_reply_to'])
-            EMAIL_SERVER_HOSTNAME = get_input("What is the email server hostname?", defaults['email_server_hostname'])
-            try:
-                EMAIL_SERVER_PORT = int(get_input("What is the email server port?", defaults['email_server_port']))
-            except ValueError:
-                EMAIL_SERVER_PORT = defaults['email_server_port']
-            EMAIL_INTERNAL_DOMAIN = get_input("What is the internal email address format?", defaults['email_internal_domain'])
-            break
-
-        elif (is_email_enabled.lower() in ['no', 'n']):
-            EMAIL_ENABLED = False
-            EMAIL_USER = defaults['email_user']
-            EMAIL_PASSWORD = defaults['email_password']
-            EMAIL_SENDER = defaults['email_sender']
-            EMAIL_REPLY_TO = defaults['email_reply_to']
-            EMAIL_SERVER_HOSTNAME = defaults['email_server_hostname']
-            EMAIL_SERVER_PORT = defaults['email_server_port']
-            EMAIL_INTERNAL_DOMAIN = defaults['email_internal_domain']
-            break
-    print()
-
-
+full_config = generate_config(defaults, args.worker, authentication_methods)
 
 ##############################################################################
 # make the installation setup directory
@@ -400,61 +227,30 @@ def __call__(self, parser, namespace, values, option_string=None):
 if os.path.isdir(SETUP_INSTALL_DIR):
     shutil.rmtree(SETUP_INSTALL_DIR)
 os.makedirs(SETUP_INSTALL_DIR, exist_ok=True)
-
-shutil.chown(SETUP_INSTALL_DIR, 'root', COURSE_BUILDERS_GROUP)
 os.chmod(SETUP_INSTALL_DIR, 0o751)
 
 ##############################################################################
 # WRITE CONFIG FILES IN ${SUBMITTY_INSTALL_DIR}/.setup
+config = full_config['general']
 
-config = OrderedDict()
+if args.worker: 
+    config['supervisor_user'] = config['supervisor_user']
+    with open(SUBMITTY_USERS_JSON, 'w') as json_file:
+        json.dump(config, json_file, indent=2)
 
 config['submitty_install_dir'] = SUBMITTY_INSTALL_DIR
 config['submitty_repository'] = SUBMITTY_REPOSITORY
 config['submitty_data_dir'] = SUBMITTY_DATA_DIR
-
 config['course_builders_group'] = COURSE_BUILDERS_GROUP
-
-config['num_untrusted'] = NUM_UNTRUSTED
-config['first_untrusted_uid'] = FIRST_UNTRUSTED_UID
-config['first_untrusted_gid'] = FIRST_UNTRUSTED_UID
 config['num_grading_scheduler_workers'] = NUM_GRADING_SCHEDULER_WORKERS
-
-
 config['daemon_user'] = DAEMON_USER
-config['daemon_uid'] = DAEMON_UID
-config['daemon_gid'] = DAEMON_GID
 
-if args.worker:
-    config['supervisor_user'] = SUPERVISOR_USER
-else:
+if not args.worker:
     config['php_user'] = PHP_USER
     config['cgi_user'] = CGI_USER
-    config['daemonphp_group'] = DAEMONPHP_GROUP
-    config['daemoncgi_group'] = DAEMONCGI_GROUP
-    config['daemonphpcgi_group'] = DAEMONPHPCGI_GROUP
-    config['php_uid'] = PHP_UID
-    config['php_gid'] = PHP_GID
-
-    config['database_host'] = DATABASE_HOST
-    config['database_port'] = DATABASE_PORT
-    config['database_user'] = DATABASE_USER
-    config['database_password'] = DATABASE_PASS
-    config['database_course_user'] = DATABASE_COURSE_USER
-    config['database_course_password'] = DATABASE_COURSE_PASSWORD
-    config['timezone'] = TIMEZONE
-    config['default_locale'] = DEFAULT_LOCALE
-
-    config['authentication_method'] = AUTHENTICATION_METHOD
-    config['vcs_url'] = VCS_URL
-    config['submission_url'] = SUBMISSION_URL
-    config['cgi_url'] = CGI_URL
+    
     config['websocket_port'] = WEBSOCKET_PORT
-
-    config['institution_name'] = INSTITUTION_NAME
-    config['institution_homepage'] = INSTITUTION_HOMEPAGE
     config['debugging_enabled'] = DEBUGGING_ENABLED
-    config['user_create_account'] = USER_CREATE_ACCOUNT
 
 # site_log_path is a holdover name. This could more accurately be called the "log_path"
 config['site_log_path'] = TAGRADING_LOG_PATH
@@ -498,43 +294,6 @@ def write(x=''):
 except FileNotFoundError:
     pass
 
-#Rescue the autograding_workers and _containers files if they exist.
-rescued = list()
-tmp_folder = tempfile.mkdtemp()
-if not args.worker:
-    for full_file_name, file_name in [(WORKERS_JSON, 'autograding_workers.json'), (CONTAINERS_JSON, 'autograding_containers.json')]:
-        if os.path.isfile(full_file_name):
-            #make a tmp folder and copy autograding workers to it
-            tmp_file = os.path.join(tmp_folder, file_name)
-            shutil.move(full_file_name, tmp_file)
-            rescued.append((full_file_name, tmp_file))
-
-IGNORED_FILES_AND_DIRS = ['saml', 'login.md']
-
-if os.path.isdir(CONFIG_INSTALL_DIR):
-    for file in os.scandir(CONFIG_INSTALL_DIR):
-        if file.name not in IGNORED_FILES_AND_DIRS:
-            if file.is_file():
-                os.remove(os.path.join(CONFIG_INSTALL_DIR, file.name))
-            else:
-                os.rmdir(os.path.join(CONFIG_INSTALL_DIR, file.name))
-elif os.path.exists(CONFIG_INSTALL_DIR):
-    os.remove(CONFIG_INSTALL_DIR)
-os.makedirs(CONFIG_INSTALL_DIR, exist_ok=True)
-shutil.chown(CONFIG_INSTALL_DIR, 'root', COURSE_BUILDERS_GROUP)
-os.chmod(CONFIG_INSTALL_DIR, 0o755)
-
-# Finish rescuing files.
-for full_file_name, tmp_file_name in rescued:
-    #copy autograding workers back
-    shutil.move(tmp_file_name, full_file_name)
-    #make sure the permissions are correct.
-    shutil.chown(full_file_name, 'root', DAEMON_GID)
-    os.chmod(full_file_name, 0o660)
-
-#remove the tmp folder
-os.removedirs(tmp_folder)
-
 ##############################################################################
 # WRITE CONFIG FILES IN ${SUBMITTY_INSTALL_DIR}/config
 
@@ -589,99 +348,39 @@ def write(x=''):
     for file in [WORKERS_JSON, CONTAINERS_JSON]:
       os.chmod(file, 0o660)
 
-    shutil.chown(WORKERS_JSON, PHP_USER, DAEMON_GID)
-    shutil.chown(CONTAINERS_JSON, group=DAEMONPHP_GROUP)
-
 ##############################################################################
 # Write database json
 
 if not args.worker:
-    config = OrderedDict()
-    config['authentication_method'] = AUTHENTICATION_METHOD
-    config['database_host'] = DATABASE_HOST
-    config['database_port'] = DATABASE_PORT
-    config['database_user'] = DATABASE_USER
-    config['database_password'] = DATABASE_PASS
-    config['database_course_user'] = DATABASE_COURSE_USER
-    config['database_course_password'] = DATABASE_COURSE_PASSWORD
-    config['debugging_enabled'] = DEBUGGING_ENABLED
-
+    database_config = full_config['database']
+    database_config['debugging_enabled'] = DEBUGGING_ENABLED
     with open(DATABASE_JSON, 'w') as json_file:
-        json.dump(config, json_file, indent=2)
-    shutil.chown(DATABASE_JSON, 'root', DAEMONPHP_GROUP)
+        json.dump(database_config, json_file, indent=2)
     os.chmod(DATABASE_JSON, 0o440)
 
 ##############################################################################
 # Write authentication json
 if not args.worker:
-    config = OrderedDict()
-    config['authentication_method'] = AUTHENTICATION_METHOD
-    config['ldap_options'] = LDAP_OPTIONS
-    config['saml_options'] = SAML_OPTIONS
-
+    auth_config = full_config['authentication']
     with open(AUTHENTICATION_JSON, 'w') as json_file:
-        json.dump(config, json_file, indent=4)
-    shutil.chown(AUTHENTICATION_JSON, 'root', DAEMONPHP_GROUP)
+        json.dump(auth_config, json_file, indent=4)
     os.chmod(AUTHENTICATION_JSON, 0o440)
 
 ##############################################################################
-# Write submitty json
-# Full documentation at submitty.org/...
-user_id_requirements = {
-    "any_user_id": True,
-    "require_name": False,
-    "min_length": 6,
-    "max_length": 25,
-    # Example for Alyssa Hacker : hackal -- Allows for shorter names. If they are shorter, then it will just take the entire name. 
-    # Example for Joseph Wo : wojo
-    "name_requirements": {
-        "given_first": False,
-        "given_name": 2,
-        "family_name": 4
-    },
-    "require_email": False,
-    # If the user_id must contain part of the email. If whole_email is true, it must match the email.
-    # If whole_prefix is true, then the user_id must equal everything before the final @ sign.
-    # Else, it must be a certain number of characters of the prefix. 
-    # Examples for myemail@email.com:
-    # Whole email: myemail@gmail.com
-    # Whole prefix: myemail
-    # Part of prefix: myemai
-    "email_requirements": {
-        "whole_email": False,
-        "whole_prefix": False,
-        "prefix_count": 6
-    },
-    "accepted_emails": [
-        "gmail.com"
-    ]
-}
-
 
 config = submitty_config
+generated_submitty_config = full_config['submitty']
+config.update(generated_submitty_config)
 config['submitty_install_dir'] = SUBMITTY_INSTALL_DIR
 config['submitty_repository'] = SUBMITTY_REPOSITORY
 config['submitty_data_dir'] = SUBMITTY_DATA_DIR
 config['autograding_log_path'] = AUTOGRADING_LOG_PATH
-if not args.worker:
-    config['sys_admin_email'] = SYS_ADMIN_EMAIL
-    config['sys_admin_url'] = SYS_ADMIN_URL
 # site_log_path is a holdover name. This could more accurately be called the "log_path"
 config['site_log_path'] = TAGRADING_LOG_PATH
 
 if not args.worker:
-    config['submission_url'] = SUBMISSION_URL
-    config['vcs_url'] = VCS_URL
-    config['cgi_url'] = CGI_URL
     config['websocket_port'] = WEBSOCKET_PORT
-    config['institution_name'] = INSTITUTION_NAME
-    config['institution_homepage'] = INSTITUTION_HOMEPAGE
-    config['timezone'] = TIMEZONE
-    config['default_locale'] = DEFAULT_LOCALE
     config['duck_special_effects'] = False
-    config['course_material_file_upload_limit_mb'] = COURSE_MATERIAL_UPLOAD_LIMIT_MB
-    config['user_create_account'] = USER_CREATE_ACCOUNT
-    config['user_id_requirements'] = user_id_requirements
     
 config['worker'] = True if args.worker == 1 else False
 
@@ -689,36 +388,6 @@ def write(x=''):
     json.dump(config, json_file, indent=2)
 os.chmod(SUBMITTY_JSON, 0o444)
 
-##############################################################################
-# Write users json
-
-config = OrderedDict()
-config['num_grading_scheduler_workers'] = NUM_GRADING_SCHEDULER_WORKERS
-config['num_untrusted'] = NUM_UNTRUSTED
-config['first_untrusted_uid'] = FIRST_UNTRUSTED_UID
-config['first_untrusted_gid'] = FIRST_UNTRUSTED_UID
-config['daemon_uid'] = DAEMON_UID
-config['daemon_gid'] = DAEMON_GID
-config['daemon_user'] = DAEMON_USER
-config['course_builders_group'] = COURSE_BUILDERS_GROUP
-
-if not args.worker:
-    config['php_uid'] = PHP_UID
-    config['php_gid'] = PHP_GID
-    config['php_user'] = PHP_USER
-    config['cgi_user'] = CGI_USER
-    config['daemonphp_group'] = DAEMONPHP_GROUP
-    config['daemoncgi_group'] = DAEMONCGI_GROUP
-    config['daemonphpcgi_group'] = DAEMONPHPCGI_GROUP
-else:
-    config['supervisor_user'] = SUPERVISOR_USER
-
-with open(SUBMITTY_USERS_JSON, 'w') as json_file:
-    json.dump(config, json_file, indent=2)
-shutil.chown(SUBMITTY_USERS_JSON, 'root', DAEMON_GROUP if args.worker else DAEMONPHP_GROUP)
-
-os.chmod(SUBMITTY_USERS_JSON, 0o440)
-
 ##############################################################################
 # Write secrets_submitty_php json
 
@@ -728,7 +397,6 @@ def write(x=''):
     config['session'] = ''.join(secrets.choice(characters) for _ in range(64))
     with open(SECRETS_PHP_JSON, 'w') as json_file:
         json.dump(config, json_file, indent=2)
-    shutil.chown(SECRETS_PHP_JSON, 'root', PHP_GROUP)
     os.chmod(SECRETS_PHP_JSON, 0o440)
 
 ##############################################################################
@@ -736,30 +404,19 @@ def write(x=''):
 
 if not args.worker:
     config = OrderedDict()
-    config['submitty_admin_username'] = SUBMITTY_ADMIN_USERNAME
+    config['submitty_admin_username'] = full_config['admin_username']
 
     with open(SUBMITTY_ADMIN_JSON, 'w') as json_file:
         json.dump(config, json_file, indent=2)
-    shutil.chown(SUBMITTY_ADMIN_JSON, 'root', DAEMON_GROUP)
     os.chmod(SUBMITTY_ADMIN_JSON, 0o440)
 
 ##############################################################################
 # Write email json
 
 if not args.worker:
-    config = OrderedDict()
-    config['email_enabled'] = EMAIL_ENABLED
-    config['email_user'] = EMAIL_USER
-    config['email_password'] = EMAIL_PASSWORD
-    config['email_sender'] = EMAIL_SENDER
-    config['email_reply_to'] = EMAIL_REPLY_TO
-    config['email_server_hostname'] = EMAIL_SERVER_HOSTNAME
-    config['email_server_port'] = EMAIL_SERVER_PORT
-    config['email_internal_domain'] = EMAIL_INTERNAL_DOMAIN
-
+    config = full_config['email']
     with open(EMAIL_JSON, 'w') as json_file:
         json.dump(config, json_file, indent=2)
-    shutil.chown(EMAIL_JSON, 'root', DAEMONPHP_GROUP)
     os.chmod(EMAIL_JSON, 0o440)
 
 ##############################################################################
@@ -768,4 +425,4 @@ def write(x=''):
 print(f'    sudo {INSTALL_FILE}')
 print('          or')
 print(f'    sudo {INSTALL_FILE} clean')
-print("\n")
+print("\n")
\ No newline at end of file
diff --git a/.setup/GENERATE_CONFIGS.py b/.setup/GENERATE_CONFIGS.py
new file mode 100644
index 00000000000..13b3894de97
--- /dev/null
+++ b/.setup/GENERATE_CONFIGS.py
@@ -0,0 +1,226 @@
+from collections import OrderedDict
+import os
+
+def get_input(question, default=""):
+    add = "[{}] ".format(default) if default != "" else ""
+    user = input("{}: {}".format(question, add)).strip()
+    if user == "":
+        user = default
+    return user
+
+def generate_config(defaults, worker, authentication_methods):
+    print('Hit enter to use default in []')
+    print()
+        
+    if worker:
+        SUPERVISOR_USER = get_input('What is the id for your submitty user?', defaults['supervisor_user'])
+        print('SUPERVISOR USER : {}'.format(SUPERVISOR_USER))
+    else:
+        DATABASE_HOST = get_input('What is the database host?', defaults['database_host'])
+        print(DATABASE_HOST)
+
+        if not os.path.isdir(DATABASE_HOST):
+            DATABASE_PORT = int(get_input('What is the database port?', defaults['database_port']))
+            print()
+        else:
+            DATABASE_PORT = defaults['database_port']
+
+        DATABASE_USER = get_input('What is the global database user/role?', defaults['database_user'])
+        print()
+
+        default = ''
+        if 'database_password' in defaults and DATABASE_USER == defaults['database_user']:
+            default = '(Leave blank to use same password)'
+        DATABASE_PASS = get_input('What is the password for the global database user/role {}? {}'.format(DATABASE_USER, default))
+        if DATABASE_PASS == '' and DATABASE_USER == defaults['database_user'] and 'database_password' in defaults:
+            DATABASE_PASS = defaults['database_password']
+        print()
+
+        DATABASE_COURSE_USER = get_input('What is the course database user/role?', defaults['database_course_user'])
+        print()
+
+        default = ''
+        if 'database_course_password' in defaults and DATABASE_COURSE_USER == defaults['database_course_user']:
+            default = '(Leave blank to use same password)'
+        DATABASE_COURSE_PASSWORD = get_input('What is the password for the course database user/role {}? {}'.format(DATABASE_COURSE_USER, default))
+        if DATABASE_COURSE_PASSWORD == '' and DATABASE_COURSE_USER == defaults['database_course_user'] and 'database_course_password' in defaults:
+            DATABASE_COURSE_PASSWORD = defaults['database_course_password']
+        print()
+
+        TIMEZONE = get_input('What timezone should Submitty use? (for a full list of supported timezones see http://php.net/manual/en/timezones.php)', defaults['timezone'])
+        print()
+
+        DEFAULT_LOCALE = get_input('What default language should the Submitty site use?', 'en_US')
+        print()
+
+        COURSE_MATERIAL_UPLOAD_LIMIT_MB = get_input('What is the maximum file upload size for course materials (in MB)?', defaults['course_material_file_upload_limit_mb'])
+        print()
+
+        SUBMISSION_URL = get_input('What is the url for submission? (ex: http://192.168.56.101 or '
+                                'https://submitty.cs.rpi.edu)', defaults['submission_url']).rstrip('/')
+        print()
+
+        VCS_URL = get_input('What is the url for VCS? (Leave blank to default to submission url + {$vcs_type}) (ex: http://192.168.56.101/{$vcs_type} or https://submitty-vcs.cs.rpi.edu/{$vcs_type}', defaults['vcs_url']).rstrip('/')
+        print()
+
+        INSTITUTION_NAME = get_input('What is the name of your institution? (Leave blank/type "none" if not desired)',
+                                defaults['institution_name'])
+        print()
+
+        if INSTITUTION_NAME == '' or INSTITUTION_NAME.isspace():
+            INSTITUTION_HOMEPAGE = ''
+        else:
+            INSTITUTION_HOMEPAGE = get_input("What is the url of your institution\'s homepage? "
+                                        '(Leave blank/type "none" if not desired)', defaults['institution_homepage'])
+            if INSTITUTION_HOMEPAGE.lower() == "none":
+                INSTITUTION_HOMEPAGE = ''
+            print()
+        
+        SYS_ADMIN_EMAIL = get_input("What is the email for system administration?", defaults['sys_admin_email'])
+        SYS_ADMIN_URL = get_input("Where to report problems with Submitty (url for help link)?", defaults['sys_admin_url'])
+
+        print('What authentication method to use:')
+        for i in range(len(authentication_methods)):
+            print(f"{i + 1}. {authentication_methods[i]}")
+
+        while True:
+            try:
+                auth = int(get_input('Enter number?', defaults['authentication_method'])) - 1
+            except ValueError:
+                auth = -1
+            if auth in range(len(authentication_methods)):
+                break
+            print(f'Number must in between 1 - {len(authentication_methods)} (inclusive)!')
+        print()
+
+        AUTHENTICATION_METHOD = authentication_methods[auth]
+
+        default_auth_options = defaults.get('ldap_options', dict())
+        LDAP_OPTIONS = {
+            'url': default_auth_options.get('url', ''),
+            'uid': default_auth_options.get('uid', ''),
+            'bind_dn': default_auth_options.get('bind_dn', '')
+        }
+        USER_CREATE_ACCOUNT = False
+        if AUTHENTICATION_METHOD == 'DatabaseAuthentication':
+            user_create_account = get_input("Allow users to create their own accounts? [y/n]", 'n')
+            USER_CREATE_ACCOUNT = user_create_account.lower() in ['yes', 'y']
+            print()
+        if AUTHENTICATION_METHOD == 'LdapAuthentication':
+            LDAP_OPTIONS['url'] = get_input('Enter LDAP url?', LDAP_OPTIONS['url'])
+            LDAP_OPTIONS['uid'] = get_input('Enter LDAP UID?', LDAP_OPTIONS['uid'])
+            LDAP_OPTIONS['bind_dn'] = get_input('Enter LDAP bind_dn?', LDAP_OPTIONS['bind_dn'])
+
+        default_auth_options = defaults.get('saml_options', dict())
+        SAML_OPTIONS = {
+            'name': default_auth_options.get('name', ''),
+            'username_attribute': default_auth_options.get('username_attribute', '')
+        }
+
+        if AUTHENTICATION_METHOD == 'SamlAuthentication':
+            SAML_OPTIONS['name'] = get_input('Enter name you would like shown to user for authentication?', SAML_OPTIONS['name'])
+            SAML_OPTIONS['username_attribute'] = get_input('Enter SAML username attribute?', SAML_OPTIONS['username_attribute'])
+
+
+        CGI_URL = SUBMISSION_URL + '/cgi-bin'
+
+        SUBMITTY_ADMIN_USERNAME = get_input("What is the submitty admin username (optional)?", defaults['submitty_admin_username'])
+
+        while True:
+            is_email_enabled = get_input("Will Submitty use email notifications? [y/n]", 'y')
+            if (is_email_enabled.lower() in ['yes', 'y']):
+                EMAIL_ENABLED = True
+                EMAIL_USER = get_input("What is the email user?", defaults['email_user'])
+                EMAIL_PASSWORD = get_input("What is the email password",defaults['email_password'])
+                EMAIL_SENDER = get_input("What is the email sender address (the address that will appear in the From: line)?",defaults['email_sender'])
+                EMAIL_REPLY_TO = get_input("What is the email reply to address?", defaults['email_reply_to'])
+                EMAIL_SERVER_HOSTNAME = get_input("What is the email server hostname?", defaults['email_server_hostname'])
+                try:
+                    EMAIL_SERVER_PORT = int(get_input("What is the email server port?", defaults['email_server_port']))
+                except ValueError:
+                    EMAIL_SERVER_PORT = defaults['email_server_port']
+                EMAIL_INTERNAL_DOMAIN = get_input("What is the internal email address format?", defaults['email_internal_domain'])
+                break
+
+            elif (is_email_enabled.lower() in ['no', 'n']):
+                EMAIL_ENABLED = False
+                EMAIL_USER = defaults['email_user']
+                EMAIL_PASSWORD = defaults['email_password']
+                EMAIL_SENDER = defaults['email_sender']
+                EMAIL_REPLY_TO = defaults['email_reply_to']
+                EMAIL_SERVER_HOSTNAME = defaults['email_server_hostname']
+                EMAIL_SERVER_PORT = defaults['email_server_port']
+                EMAIL_INTERNAL_DOMAIN = defaults['email_internal_domain']
+                break
+        print()
+        full_config = OrderedDict()
+        general_config = OrderedDict()
+        database_config = OrderedDict()
+        authentication_config = OrderedDict()
+        submitty_config = OrderedDict()
+        email_config = OrderedDict()
+        if worker:
+            general_config['supervisor_user'] = SUPERVISOR_USER
+            
+        else: 
+
+            general_config['database_host'] = DATABASE_HOST
+            general_config['database_port'] = DATABASE_PORT
+            general_config['database_user'] = DATABASE_USER
+            general_config['database_password'] = DATABASE_PASS
+            general_config['database_course_user'] = DATABASE_COURSE_USER
+            general_config['database_course_password'] = DATABASE_COURSE_PASSWORD
+            general_config['timezone'] = TIMEZONE
+            general_config['default_locale'] = DEFAULT_LOCALE
+
+            general_config['authentication_method'] = AUTHENTICATION_METHOD
+            general_config['vcs_url'] = VCS_URL
+            general_config['submission_url'] = SUBMISSION_URL
+            general_config['cgi_url'] = CGI_URL
+            
+            general_config['institution_name'] = INSTITUTION_NAME
+            general_config['institution_homepage'] = INSTITUTION_HOMEPAGE
+            general_config['user_create_account'] = USER_CREATE_ACCOUNT
+            
+            database_config['authentication_method'] = AUTHENTICATION_METHOD
+            database_config['database_host'] = DATABASE_HOST
+            database_config['database_port'] = DATABASE_PORT
+            database_config['database_user'] = DATABASE_USER
+            database_config['database_password'] = DATABASE_PASS
+            database_config['database_course_user'] = DATABASE_COURSE_USER
+            database_config['database_course_password'] = DATABASE_COURSE_PASSWORD
+            
+            authentication_config['authentication_method'] = AUTHENTICATION_METHOD
+            authentication_config['ldap_options'] = LDAP_OPTIONS
+            authentication_config['saml_options'] = SAML_OPTIONS
+
+            submitty_config['sys_admin_email'] = SYS_ADMIN_EMAIL
+            submitty_config['sys_admin_url'] = SYS_ADMIN_URL
+            submitty_config['submission_url'] = SUBMISSION_URL
+            submitty_config['vcs_url'] = VCS_URL
+            submitty_config['cgi_url'] = CGI_URL
+            submitty_config['institution_name'] = INSTITUTION_NAME
+            submitty_config['institution_homepage'] = INSTITUTION_HOMEPAGE
+            submitty_config['timezone'] = TIMEZONE
+            submitty_config['default_locale'] = DEFAULT_LOCALE
+
+            submitty_config['course_material_file_upload_limit_mb'] = COURSE_MATERIAL_UPLOAD_LIMIT_MB
+            submitty_config['user_create_account'] = USER_CREATE_ACCOUNT
+            submitty_config['user_id_requirements'] = defaults['user_id_requirements']
+                
+            email_config['email_enabled'] = EMAIL_ENABLED
+            email_config['email_user'] = EMAIL_USER
+            email_config['email_password'] = EMAIL_PASSWORD
+            email_config['email_sender'] = EMAIL_SENDER
+            email_config['email_reply_to'] = EMAIL_REPLY_TO
+            email_config['email_server_hostname'] = EMAIL_SERVER_HOSTNAME
+            email_config['email_server_port'] = EMAIL_SERVER_PORT
+            email_config['email_internal_domain'] = EMAIL_INTERNAL_DOMAIN
+
+            full_config['database'] = database_config
+            full_config['authentication'] = authentication_config
+            full_config['submitty'] = submitty_config
+            full_config['general'] = general_config
+            full_config['email'] = email_config
+            full_config['admin_username'] = SUBMITTY_ADMIN_USERNAME
+    return full_config
\ No newline at end of file
diff --git a/.setup/USERS_SETUP.py b/.setup/USERS_SETUP.py
new file mode 100644
index 00000000000..fa504c034fd
--- /dev/null
+++ b/.setup/USERS_SETUP.py
@@ -0,0 +1,202 @@
+#!/usr/bin/env python3
+
+import argparse
+import grp
+import json
+import pwd
+from collections import OrderedDict
+import shutil
+import tempfile
+import os
+
+def get_uid(user):
+    return pwd.getpwnam(user).pw_uid
+
+
+def get_gid(user):
+    return pwd.getpwnam(user).pw_gid
+
+
+def get_ids(user):
+    try:
+        return get_uid(user), get_gid(user)
+    except KeyError:
+        raise SystemExit("ERROR: Could not find user: " + user)
+
+parser = argparse.ArgumentParser(description='Submitty configuration script',
+                                 formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+parser.add_argument('--worker', action='store_true', default=False, help='Configure Submitty with autograding only')
+parser.add_argument('--install-dir', default='/usr/local/submitty', help='Set the install directory for Submitty')
+args = parser.parse_args()
+
+##########################################################
+
+# recommended names for special users & groups related to the SUBMITTY system
+PHP_USER = 'submitty_php'
+PHP_GROUP = 'submitty_php'
+CGI_USER = 'submitty_cgi'
+DAEMON_USER = 'submitty_daemon'
+DAEMON_GROUP = 'submitty_daemon'
+COURSE_BUILDERS_GROUP = 'submitty_course_builders'
+
+##############################################################################
+
+# adjust this number depending on the # of processors
+# available on your hardware
+NUM_GRADING_SCHEDULER_WORKERS = 5
+
+##############################################################################
+
+SETUP_INSTALL_DIR = os.path.join(args.install_dir, '.setup')
+
+INSTALL_FILE = os.path.join(SETUP_INSTALL_DIR, 'INSTALL_SUBMITTY.sh')
+CONFIGURATION_JSON = os.path.join(SETUP_INSTALL_DIR, 'submitty_conf.json')
+CONFIG_INSTALL_DIR = os.path.join(args.install_dir, 'config')
+
+EMAIL_JSON = os.path.join(CONFIG_INSTALL_DIR, 'email.json')
+AUTHENTICATION_JSON = os.path.join(CONFIG_INSTALL_DIR, 'authentication.json')
+DATABASE_JSON = os.path.join(CONFIG_INSTALL_DIR, 'database.json')
+SUBMITTY_JSON = os.path.join(CONFIG_INSTALL_DIR, 'submitty.json')
+SUBMITTY_USERS_JSON = os.path.join(CONFIG_INSTALL_DIR, 'submitty_users.json')
+WORKERS_JSON = os.path.join(CONFIG_INSTALL_DIR, 'autograding_workers.json')
+SUBMITTY_ADMIN_JSON = os.path.join(CONFIG_INSTALL_DIR, 'submitty_admin.json')
+CONTAINERS_JSON = os.path.join(CONFIG_INSTALL_DIR, 'autograding_containers.json')
+SECRETS_PHP_JSON = os.path.join(CONFIG_INSTALL_DIR, 'secrets_submitty_php.json')
+
+if not args.worker:
+    PHP_UID, PHP_GID = get_ids(PHP_USER)
+    CGI_UID, CGI_GID = get_ids(CGI_USER)
+    # System Groups
+    DAEMONPHP_GROUP = 'submitty_daemonphp'
+    try:
+        grp.getgrnam(DAEMONPHP_GROUP)
+    except KeyError:
+        raise SystemExit("ERROR: Could not find group: " + DAEMONPHP_GROUP)
+    DAEMONCGI_GROUP = 'submitty_daemoncgi'
+    try:
+        grp.getgrnam(DAEMONCGI_GROUP)
+    except KeyError:
+        raise SystemExit("ERROR: Could not find group: " + DAEMONCGI_GROUP)
+    DAEMONPHPCGI_GROUP = 'submitty_daemonphpcgi'
+    try:
+        grp.getgrnam(DAEMONPHPCGI_GROUP)
+    except KeyError:
+        raise SystemExit("ERROR: Could not find group: " + DAEMONPHPCGI_GROUP)
+
+DAEMON_UID, DAEMON_GID = get_ids(DAEMON_USER)
+
+
+try:
+    grp.getgrnam(COURSE_BUILDERS_GROUP)
+except KeyError:
+    raise SystemExit("ERROR: Could not find group: " + COURSE_BUILDERS_GROUP)
+
+##############################################################################
+
+# This is the upper limit of the number of parallel grading threads on
+# this machine
+NUM_UNTRUSTED = 60
+
+FIRST_UNTRUSTED_UID, FIRST_UNTRUSTED_GID = get_ids('untrusted00')
+
+# confirm that the uid/gid of the untrusted users are sequential
+for i in range(1, NUM_UNTRUSTED):
+    untrusted_user = "untrusted{:0=2d}".format(i)
+    uid, gid = get_ids(untrusted_user)
+    if uid != FIRST_UNTRUSTED_UID + i:
+        raise SystemExit('CONFIGURATION ERROR: untrusted UID not sequential: ' + untrusted_user)
+    elif gid != FIRST_UNTRUSTED_GID + i:
+        raise SystemExit('CONFIGURATION ERROR: untrusted GID not sequential: ' + untrusted_user)
+
+with open(SUBMITTY_JSON, 'r') as json_file:
+    config = json.load(json_file, object_pairs_hook=OrderedDict)
+    config['num_untrusted'] = NUM_UNTRUSTED
+    config['first_untrusted_uid'] = FIRST_UNTRUSTED_UID
+    config['first_untrusted_gid'] = FIRST_UNTRUSTED_UID
+
+    config['daemon_uid'] = DAEMON_UID
+    config['daemon_gid'] = DAEMON_GID
+
+    # not worker
+    config['daemonphp_group'] = DAEMONPHP_GROUP
+    config['daemoncgi_group'] = DAEMONCGI_GROUP
+    config['daemonphpcgi_group'] = DAEMONPHPCGI_GROUP
+    config['php_uid'] = PHP_UID
+    config['php_gid'] = PHP_GID
+
+#Rescue the autograding_workers and _containers files if they exist.
+rescued = list()
+tmp_folder = tempfile.mkdtemp()
+if not args.worker:
+    for full_file_name, file_name in [(WORKERS_JSON, 'autograding_workers.json'), (CONTAINERS_JSON, 'autograding_containers.json')]:
+        if os.path.isfile(full_file_name):
+            #make a tmp folder and copy autograding workers to it
+            tmp_file = os.path.join(tmp_folder, file_name)
+            shutil.move(full_file_name, tmp_file)
+            rescued.append((full_file_name, tmp_file))
+
+IGNORED_FILES_AND_DIRS = ['saml', 'login.md']
+
+if os.path.isdir(CONFIG_INSTALL_DIR):
+    for file in os.scandir(CONFIG_INSTALL_DIR):
+        if file.name not in IGNORED_FILES_AND_DIRS:
+            if file.is_file():
+                os.remove(os.path.join(CONFIG_INSTALL_DIR, file.name))
+            else:
+                os.rmdir(os.path.join(CONFIG_INSTALL_DIR, file.name))
+elif os.path.exists(CONFIG_INSTALL_DIR):
+    os.remove(CONFIG_INSTALL_DIR)
+os.makedirs(CONFIG_INSTALL_DIR, exist_ok=True)
+shutil.chown(CONFIG_INSTALL_DIR, 'root', COURSE_BUILDERS_GROUP)
+os.chmod(CONFIG_INSTALL_DIR, 0o755)
+
+# Finish rescuing files.
+for full_file_name, tmp_file_name in rescued:
+    #copy autograding workers back
+    shutil.move(tmp_file_name, full_file_name)
+    #make sure the permissions are correct.
+    shutil.chown(full_file_name, 'root', DAEMON_GID)
+    os.chmod(full_file_name, 0o660)
+
+#remove the tmp folder
+os.removedirs(tmp_folder)
+
+##############################################################################
+# Write users json
+
+config = OrderedDict()
+config['num_grading_scheduler_workers'] = NUM_GRADING_SCHEDULER_WORKERS
+config['num_untrusted'] = NUM_UNTRUSTED
+config['first_untrusted_uid'] = FIRST_UNTRUSTED_UID
+config['first_untrusted_gid'] = FIRST_UNTRUSTED_UID
+config['daemon_uid'] = DAEMON_UID
+config['daemon_gid'] = DAEMON_GID
+config['daemon_user'] = DAEMON_USER
+config['course_builders_group'] = COURSE_BUILDERS_GROUP
+
+if not args.worker:
+    config['php_uid'] = PHP_UID
+    config['php_gid'] = PHP_GID
+    config['php_user'] = PHP_USER
+    config['cgi_user'] = CGI_USER
+    config['daemonphp_group'] = DAEMONPHP_GROUP
+    config['daemoncgi_group'] = DAEMONCGI_GROUP
+    config['daemonphpcgi_group'] = DAEMONPHPCGI_GROUP
+if os.path.exists(SUBMITTY_USERS_JSON):
+    with open(SUBMITTY_USERS_JSON, 'r') as json_file:
+        config_file = json.load(json_file)
+        config['supervisor_user'] = config_file['supervisor_user']
+with open(SUBMITTY_USERS_JSON, 'w') as json_file:
+    json.dump(config, json_file, indent=2)
+shutil.chown(SUBMITTY_USERS_JSON, 'root', DAEMON_GROUP if args.worker else DAEMONPHP_GROUP)
+
+os.chmod(SUBMITTY_USERS_JSON, 0o440)
+shutil.chown(WORKERS_JSON, PHP_USER, DAEMON_GID)
+shutil.chown(CONTAINERS_JSON, group=DAEMONPHP_GROUP)
+shutil.chown(DATABASE_JSON, 'root', DAEMONPHP_GROUP)
+shutil.chown(AUTHENTICATION_JSON, 'root', DAEMONPHP_GROUP)
+shutil.chown(EMAIL_JSON, 'root', DAEMONPHP_GROUP)
+shutil.chown(SECRETS_PHP_JSON, 'root', PHP_GROUP)
+shutil.chown(SUBMITTY_ADMIN_JSON, 'root', DAEMON_GROUP)
+shutil.chown(SETUP_INSTALL_DIR, 'root', COURSE_BUILDERS_GROUP)
+shutil.chown(CONFIG_INSTALL_DIR, 'root', COURSE_BUILDERS_GROUP)
\ No newline at end of file
diff --git a/.setup/distro_setup/ubuntu/22.04/variables.sh b/.setup/distro_setup/ubuntu/22.04/variables.sh
new file mode 100644
index 00000000000..80edc76c777
--- /dev/null
+++ b/.setup/distro_setup/ubuntu/22.04/variables.sh
@@ -0,0 +1,6 @@
+if [ ${DEV_VM} == 1 ]; then
+    export SUBMISSION_URL='http://localhost:1511'
+    export SUBMISSION_PORT=1511
+    export DATABASE_PORT=16442
+    export WEBSOCKET_PORT=8443
+fi
diff --git a/.setup/distro_setup/variables.sh b/.setup/distro_setup/variables.sh
new file mode 100644
index 00000000000..42a8cf03d97
--- /dev/null
+++ b/.setup/distro_setup/variables.sh
@@ -0,0 +1,20 @@
+#!/usr/bin/env bash
+
+# this script must be run by root or sudo
+if [[ "$UID" -ne "0" ]] ; then
+    echo "ERROR: This script must be run by root or sudo"
+    exit
+fi
+
+# Note: This script is source by install_system.sh and so caution should be used on naming variables
+# to ensure there is no collision.
+SETUP_DISTRO_DIR="$( cd -P "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+DISTRO=$(lsb_release -si | tr '[:upper:]' '[:lower:]')
+VERSION=$(lsb_release -sr | tr '[:upper:]' '[:lower:]')
+
+if [ ! -d ${SETUP_DISTRO_DIR}/${DISTRO}/${VERSION} ]; then
+    (>&2 echo "Unknown distro: ${DISTRO} ${VERSION}")
+    exit 1
+fi
+
+source ${SETUP_DISTRO_DIR}/${DISTRO}/${VERSION}/variables.sh
diff --git a/.setup/install_system.sh b/.setup/install_system.sh
index 2263d1373c2..0babff05a63 100644
--- a/.setup/install_system.sh
+++ b/.setup/install_system.sh
@@ -41,6 +41,12 @@ LICHEN_REPOSITORY=/usr/local/submitty/GIT_CHECKOUT/Lichen
 SUBMITTY_INSTALL_DIR=/usr/local/submitty
 SUBMITTY_DATA_DIR=/var/local/submitty
 
+# create directory and fix permissions
+mkdir -p ${SUBMITTY_DATA_DIR}
+mkdir -p ${SUBMITTY_INSTALL_DIR}/config
+INSTALL_SYS_DIR=$(mktemp -d)
+chmod 777 "${INSTALL_SYS_DIR}"
+pushd "${INSTALL_SYS_DIR}" > /dev/null
 
 # USERS / GROUPS
 DAEMON_USER=submitty_daemon
@@ -50,12 +56,17 @@ PHP_GROUP=submitty_php
 CGI_USER=submitty_cgi
 CGI_GROUP=submitty_cgi
 
+COURSE_BUILDERS_GROUP=submitty_course_builders
+DB_USER=submitty_dbuser
+DATABASE_PASSWORD=submitty_dbuser
+DB_COURSE_USER=submitty_course_dbuser
+DB_COURSE_PASSWORD=submitty_dbuser
+
 DAEMONPHP_GROUP=submitty_daemonphp
 DAEMONCGI_GROUP=submitty_daemoncgi
 DAEMONPHPCGI_GROUP=submitty_daemonphpcgi
 
-# VERSIONS
-source ${CURRENT_DIR}/bin/versions.sh
+
 
 #################################################################
 # PROVISION SETUP
@@ -107,6 +118,66 @@ fi
 if [ ${UTM} == 1 ]; then
     mkdir ${SUBMITTY_REPOSITORY}/.utm
 fi
+#################################################################
+# DISTRO SETUP
+#################
+# Sources
+source ${CURRENT_DIR}/bin/versions.sh
+source ${CURRENT_DIR}/distro_setup/variables.sh
+#################################################################
+# SUBMITTY SETUP
+#################
+apt-get update
+apt-get install -qqy python3 python3-pip
+pip3 install tzlocal
+#If in worker mode, run configure with --worker option.
+if [ ${WORKER} == 1 ]; then
+    echo "Running configure submitty in worker mode"
+    if [ ${DEV_VM} == 1 ]; then
+        echo "submitty" | python3 ${SUBMITTY_REPOSITORY}/.setup/CONFIGURE_SUBMITTY.py --worker
+    else
+        python3 ${SUBMITTY_REPOSITORY}/.setup/CONFIGURE_SUBMITTY.py --worker
+    fi
+else
+    if [ ${DEV_VM} == 1 ]; then
+        # This should be set by setup_distro.sh for whatever distro we have, but
+        # in case it is not, default to our primary URL
+        if [ -z "${SUBMISSION_URL}" ]; then
+            SUBMISSION_URL='http://192.168.56.101'
+        fi
+        mkdir /var/run/postgresql
+        echo -e "/var/run/postgresql
+${DB_USER}
+${DATABASE_PASSWORD}
+${DB_COURSE_USER}
+${DB_COURSE_PASSWORD}
+America/New_York
+en_US
+100
+${SUBMISSION_URL}
+
+
+sysadmin@example.com
+https://example.com
+1
+submitty-admin
+y
+
+
+submitty@vagrant
+do-not-reply@vagrant
+localhost
+25
+" | python3 ${SUBMITTY_REPOSITORY}/.setup/CONFIGURE_SUBMITTY.py --debug --setup-for-sample-courses --websocket-port ${WEBSOCKET_PORT}
+
+        # Set these manually as they're not asked about during CONFIGURE_SUBMITTY.py
+        sed -i -e 's/"url": ""/"url": "ldap:\/\/localhost"/g' ${SUBMITTY_INSTALL_DIR}/config/authentication.json
+        sed -i -e 's/"uid": ""/"uid": "uid"/g' ${SUBMITTY_INSTALL_DIR}/config/authentication.json
+        sed -i -e 's/"bind_dn": ""/"bind_dn": "ou=users,dc=vagrant,dc=local"/g' ${SUBMITTY_INSTALL_DIR}/config/authentication.json
+    else
+        python3 ${SUBMITTY_REPOSITORY}/.setup/CONFIGURE_SUBMITTY.py
+    fi
+fi
 
 if [ ${DEV_VM} == 1 ] && [ ${WORKER} == 0 ]; then
     # Setting it up to allow SSH as root by default
@@ -208,24 +279,8 @@ else
 
 fi
 
-INSTALL_SYS_DIR=$(mktemp -d)
-chmod 777 "${INSTALL_SYS_DIR}"
-pushd "${INSTALL_SYS_DIR}" > /dev/null
-
-COURSE_BUILDERS_GROUP=submitty_course_builders
-DB_USER=submitty_dbuser
-DATABASE_PASSWORD=submitty_dbuser
-DB_COURSE_USER=submitty_course_dbuser
-DB_COURSE_PASSWORD=submitty_dbuser
-
-#################################################################
-# DISTRO SETUP
-#################
-
 source ${CURRENT_DIR}/distro_setup/setup_distro.sh
 
-bash "${SUBMITTY_REPOSITORY}/.setup/update_system.sh" "config=${SUBMITTY_DIRECTORY}"
-
 #################################################################
 # STACK SETUP
 #################
@@ -349,6 +404,13 @@ sudo chown "${DAEMON_USER}:${DAEMON_USER}" "$gitconfig_path"
 
 usermod -a -G docker "${DAEMON_USER}"
 
+#If in worker mode, run configure with --worker option.
+if [ ${WORKER} == 1 ]; then
+    echo "Using users to update config files"
+    python3 ${SUBMITTY_REPOSITORY}/.setup/USERS_SETUP.py --worker
+else
+    python3 ${SUBMITTY_REPOSITORY}/.setup/USERS_SETUP.py
+fi
 #################################################################
 # JAR SETUP
 #################
@@ -576,9 +638,6 @@ EOF
     sed -i -e "s/^disable_functions = .*/disable_functions = ${DISABLED_FUNCTIONS}/g" /etc/php/${PHP_VERSION}/fpm/php.ini
 fi
 
-# create directories and fix permissions
-mkdir -p ${SUBMITTY_DATA_DIR}
-
 #Set up database and copy down the tutorial repo if not in worker mode
 if [ ${WORKER} == 0 ]; then
     # create the courses directory. This is needed for the first time we run
@@ -667,59 +726,6 @@ if [ ! -d "${clangsrc}" ]; then
     echo 'DONE PREPARING CLANG INSTALLATION'
 fi
 
-#################################################################
-# SUBMITTY SETUP
-#################
-echo Beginning Submitty Setup
-
-#If in worker mode, run configure with --worker option.
-if [ ${WORKER} == 1 ]; then
-    echo "Running configure submitty in worker mode"
-    if [ ${DEV_VM} == 1 ]; then
-        echo "submitty" | python3 ${SUBMITTY_REPOSITORY}/.setup/CONFIGURE_SUBMITTY.py --worker
-    else
-        python3 ${SUBMITTY_REPOSITORY}/.setup/CONFIGURE_SUBMITTY.py --worker
-    fi
-else
-    if [ ${DEV_VM} == 1 ]; then
-        # This should be set by setup_distro.sh for whatever distro we have, but
-        # in case it is not, default to our primary URL
-        if [ -z "${SUBMISSION_URL}" ]; then
-            SUBMISSION_URL='http://192.168.56.101'
-        fi
-        echo -e "/var/run/postgresql
-${DB_USER}
-${DATABASE_PASSWORD}
-${DB_COURSE_USER}
-${DB_COURSE_PASSWORD}
-America/New_York
-en_US
-100
-${SUBMISSION_URL}
-
-
-sysadmin@example.com
-https://example.com
-1
-submitty-admin
-y
-
-
-submitty@vagrant
-do-not-reply@vagrant
-localhost
-25
-" | python3 ${SUBMITTY_REPOSITORY}/.setup/CONFIGURE_SUBMITTY.py --debug --setup-for-sample-courses --websocket-port ${WEBSOCKET_PORT}
-
-        # Set these manually as they're not asked about during CONFIGURE_SUBMITTY.py
-        sed -i -e 's/"url": ""/"url": "ldap:\/\/localhost"/g' ${SUBMITTY_INSTALL_DIR}/config/authentication.json
-        sed -i -e 's/"uid": ""/"uid": "uid"/g' ${SUBMITTY_INSTALL_DIR}/config/authentication.json
-        sed -i -e 's/"bind_dn": ""/"bind_dn": "ou=users,dc=vagrant,dc=local"/g' ${SUBMITTY_INSTALL_DIR}/config/authentication.json
-    else
-        python3 ${SUBMITTY_REPOSITORY}/.setup/CONFIGURE_SUBMITTY.py
-    fi
-fi
-
 if [ ${WORKER} == 1 ]; then
    #Add the submitty user to /etc/sudoers if in worker mode.
     SUPERVISOR_USER=$(jq -r '.supervisor_user' ${SUBMITTY_INSTALL_DIR}/config/submitty_users.json)