diff --git a/lib/settings.js b/lib/settings.js
index 56e20e88..2da38d71 100644
--- a/lib/settings.js
+++ b/lib/settings.js
@@ -26,7 +26,7 @@ class Settings {
     return settings
   }
 
-  static async syncSubOrgs(nop, context, suborg, repo, config, ref) {
+  static async syncSubOrgs (nop, context, suborg, repo, config, ref) {
     const settings = new Settings(nop, context, repo, config, ref, suborg)
     try {
       await settings.loadConfigs()
@@ -38,7 +38,7 @@ class Settings {
     }
   }
 
-  static async sync(nop, context, repo, config, ref) {
+  static async sync (nop, context, repo, config, ref) {
     const settings = new Settings(nop, context, repo, config, ref)
     try {
       await settings.loadConfigs(repo)
@@ -53,13 +53,13 @@ class Settings {
     }
   }
 
-  static async handleError(nop, context, repo, config, ref, nopcommand) {
+  static async handleError (nop, context, repo, config, ref, nopcommand) {
     const settings = new Settings(nop, context, repo, config, ref)
     settings.appendToResults([nopcommand])
     await settings.handleResults()
   }
 
-  constructor(nop, context, repo, config, ref, suborg) {
+  constructor (nop, context, repo, config, ref, suborg) {
     this.ref = ref
     this.context = context
     this.installation_id = context.payload.installation.id
@@ -98,7 +98,7 @@ class Settings {
   }
 
   // Create a check in the Admin repo for safe-settings.
-  async createCheckRun() {
+  async createCheckRun () {
     const startTime = new Date()
     let conclusion = 'success'
     let details = `Run on: \`${new Date().toISOString()}\``
@@ -144,7 +144,7 @@ class Settings {
       })
   }
 
-  logError(msg) {
+  logError (msg) {
     this.log.error(msg)
     this.errors.push({
       owner: this.repo.owner,
@@ -154,7 +154,7 @@ class Settings {
     })
   }
 
-  async handleResults() {
+  async handleResults () {
     const { payload } = this.context
 
     // Create a checkrun if not in nop mode
@@ -164,12 +164,12 @@ class Settings {
       return
     }
 
-    //remove duplicate rows in this.results
+    // remove duplicate rows in this.results
     this.results = this.results.filter((thing, index, self) => {
-        return index === self.findIndex((t) => {
-          return t.type === thing.type && t.repo === thing.repo && t.plugin === thing.plugin
-        })
+      return index === self.findIndex((t) => {
+        return t.type === thing.type && t.repo === thing.repo && t.plugin === thing.plugin
       })
+    })
 
     let error = false
     // Different logic
@@ -281,12 +281,12 @@ ${this.results.reduce((x, y) => {
     await this.github.checks.update(params)
   }
 
-  async loadConfigs(repo) {
+  async loadConfigs (repo) {
     this.subOrgConfigs = await this.getSubOrgConfigs()
     this.repoConfigs = await this.getRepoConfigs(repo)
   }
 
-  async updateOrg() {
+  async updateOrg () {
     const rulesetsConfig = this.config.rulesets
     if (rulesetsConfig) {
       const RulesetsPlugin = Settings.PLUGINS.rulesets
@@ -296,11 +296,12 @@ ${this.results.reduce((x, y) => {
     }
   }
 
-  async updateRepos(repo) {
+  async updateRepos (repo) {
     this.subOrgConfigs = this.subOrgConfigs || await this.getSubOrgConfigs()
-    let repoConfig = this.config.repository
+    // Create a fresh copy of the base repository config
+    let repoConfig = this.config.repository ? Object.assign({}, this.config.repository) : {}
     if (repoConfig) {
-      repoConfig = Object.assign(repoConfig, { name: repo.repo, org: repo.owner })
+      repoConfig = Object.assign({}, repoConfig, { name: repo.repo, org: repo.owner })
     }
 
     const subOrgConfig = this.getSubOrgConfig(repo.repo)
@@ -314,9 +315,9 @@ ${this.results.reduce((x, y) => {
     this.log.debug(`Process normally... Not a SubOrg config change or SubOrg config was changed and this repo is part of it. ${JSON.stringify(repo)} suborg config ${JSON.stringify(this.subOrgConfigMap)}`)
 
     if (subOrgConfig) {
-      let suborgRepoConfig = subOrgConfig.repository
+      let suborgRepoConfig = subOrgConfig.repository ? Object.assign({}, subOrgConfig.repository) : {}
       if (suborgRepoConfig) {
-        suborgRepoConfig = Object.assign(suborgRepoConfig, { name: repo.repo, org: repo.owner })
+        suborgRepoConfig = Object.assign({}, suborgRepoConfig, { name: repo.repo, org: repo.owner })
         repoConfig = this.mergeDeep.mergeDeep({}, repoConfig, suborgRepoConfig)
       }
     }
@@ -327,7 +328,7 @@ ${this.results.reduce((x, y) => {
     if (overrideRepoConfig) {
       repoConfig = this.mergeDeep.mergeDeep({}, repoConfig, overrideRepoConfig)
     }
-    const {shouldContinue, nopCommands} = await new Archive(this.nop, this.github, repo, repoConfig, this.log).sync()
+    const { shouldContinue, nopCommands } = await new Archive(this.nop, this.github, repo, repoConfig, this.log).sync()
     if (nopCommands) this.appendToResults(nopCommands)
     if (shouldContinue) {
       if (repoConfig) {
@@ -366,7 +367,7 @@ ${this.results.reduce((x, y) => {
     }
   }
 
-  async updateAll() {
+  async updateAll () {
     // this.subOrgConfigs = this.subOrgConfigs || await this.getSubOrgConfigs(this.github, this.repo, this.log)
     // this.repoConfigs = this.repoConfigs || await this.getRepoConfigs(this.github, this.repo, this.log)
     return this.eachRepositoryRepos(this.github, this.log).then(res => {
@@ -374,7 +375,7 @@ ${this.results.reduce((x, y) => {
     })
   }
 
-  getSubOrgConfig(repoName) {
+  getSubOrgConfig (repoName) {
     if (this.subOrgConfigs) {
       for (const k of Object.keys(this.subOrgConfigs)) {
         const repoPattern = new Glob(k)
@@ -387,13 +388,13 @@ ${this.results.reduce((x, y) => {
   }
 
   // Remove Org specific configs from the repo config
-  returnRepoSpecificConfigs(config) {
+  returnRepoSpecificConfigs (config) {
     const newConfig = Object.assign({}, config) // clone
     delete newConfig.rulesets
     return newConfig
   }
 
-  childPluginsList(repo) {
+  childPluginsList (repo) {
     const repoName = repo.repo
     const subOrgOverrideConfig = this.getSubOrgConfig(repoName)
     this.log.debug(`suborg config for ${repoName} is ${JSON.stringify(subOrgOverrideConfig)}`)
@@ -425,11 +426,11 @@ ${this.results.reduce((x, y) => {
     return childPlugins
   }
 
-  getRepoOverrideConfig(repoName) {
+  getRepoOverrideConfig (repoName) {
     return this.repoConfigs[`${repoName}.yml`] || this.repoConfigs[`${repoName}.yaml`] || {}
   }
 
-  validate(section, baseConfig, overrideConfig) {
+  validate (section, baseConfig, overrideConfig) {
     const configValidator = this.configvalidators[section]
     if (configValidator) {
       this.log.debug(`Calling configvalidator for key ${section} `)
@@ -448,7 +449,7 @@ ${this.results.reduce((x, y) => {
     }
   }
 
-  isRestricted(repoName) {
+  isRestricted (repoName) {
     const restrictedRepos = this.config.restrictedRepos
     // Skip configuring any restricted repos
     if (Array.isArray(restrictedRepos)) {
@@ -480,7 +481,7 @@ ${this.results.reduce((x, y) => {
     return false
   }
 
-  includesRepo(repoName, restrictedRepos) {
+  includesRepo (repoName, restrictedRepos) {
     return restrictedRepos.filter((restrictedRepo) => { return RegExp(restrictedRepo).test(repoName) }).length > 0
   }
 
@@ -535,7 +536,7 @@ ${this.results.reduce((x, y) => {
    * @param params Params to fetch the file with
    * @return The parsed YAML file
    */
-  async loadConfigMap(params) {
+  async loadConfigMap (params) {
     try {
       this.log.debug(` In loadConfigMap ${JSON.stringify(params)}`)
       const response = await this.github.repos.getContent(params).catch(e => {
@@ -582,7 +583,7 @@ ${this.results.reduce((x, y) => {
    * @param params Params to fetch the file with
    * @return The parsed YAML file
    */
-  async getRepoConfigMap() {
+  async getRepoConfigMap () {
     try {
       this.log.debug(` In getRepoConfigMap ${JSON.stringify(this.repo)}`)
       // GitHub getContent api has a hard limit of returning 1000 entries without
@@ -649,7 +650,7 @@ ${this.results.reduce((x, y) => {
    * @param params Params to fetch the file with
    * @return The parsed YAML file
    */
-  async getSubOrgConfigMap() {
+  async getSubOrgConfigMap () {
     try {
       this.log.debug(` In getSubOrgConfigMap ${JSON.stringify(this.repo)}`)
       const repo = { owner: this.repo.owner, repo: env.ADMIN_REPO }
@@ -676,7 +677,7 @@ ${this.results.reduce((x, y) => {
    * @param {*} repo repo param
    * @returns repoConfigs object
    */
-  async getRepoConfigs(repo) {
+  async getRepoConfigs (repo) {
     try {
       const overridePaths = await this.getRepoConfigMap()
       const repoConfigs = {}
@@ -728,7 +729,7 @@ ${this.results.reduce((x, y) => {
    * @param params Params to fetch the file with
    * @return The parsed YAML file
    */
-  async getSubOrgConfigs() {
+  async getSubOrgConfigs () {
     try {
       // Get all suborg configs even though we might be here becuase of a suborg config change
       // we will filter them out if request is due to a suborg config change
@@ -805,7 +806,7 @@ ${this.results.reduce((x, y) => {
     }
   }
 
-  storeSubOrgConfigIfNoConflicts(subOrgConfigs, overridePath, repoName, data) {
+  storeSubOrgConfigIfNoConflicts (subOrgConfigs, overridePath, repoName, data) {
     const existingConfigForRepo = subOrgConfigs[repoName]
     if (existingConfigForRepo && existingConfigForRepo.source !== overridePath) {
       throw new Error(`Multiple suborg configs for ${repoName} in ${overridePath} and ${existingConfigForRepo?.source}`)
@@ -819,7 +820,7 @@ ${this.results.reduce((x, y) => {
    * @param params Params to fetch the file with
    * @return The parsed YAML file
    */
-  async loadYaml(filePath) {
+  async loadYaml (filePath) {
     try {
       const repo = { owner: this.repo.owner, repo: env.ADMIN_REPO }
       const params = Object.assign(repo, { path: filePath, ref: this.ref })
@@ -867,7 +868,7 @@ ${this.results.reduce((x, y) => {
     this.results = this.results.concat(results)
   }
 
-  async getReposForTeam(teamslug) {
+  async getReposForTeam (teamslug) {
     const options = this.github.rest.teams.listReposInOrg.endpoint.merge({
       org: this.repo.owner,
       team_slug: teamslug,
@@ -893,7 +894,6 @@ ${this.results.reduce((x, y) => {
       throw new Error(`Failed to filter repositories for property ${name}: ${error.message}`)
     }
   }
-  
 
   async getSubOrgRepositories (subOrgProperties) {
     const organizationName = this.repo.owner
@@ -924,7 +924,7 @@ ${this.results.reduce((x, y) => {
     return (item && typeof item === 'object' && !Array.isArray(item))
   }
 
-  isIterable(obj) {
+  isIterable (obj) {
     // checks for null and undefined
     if (obj == null) {
       return false