This is a collection of groovy scripts I gathered and use for bootstrapping Jenkins. Most of this can also be achieved with the CasC Plugin https://github.com/jenkinsci/configuration-as-code-plugin

baseURL.groovy

#!groovy

/*
 * This script configures the Jenkins base URL.
 */

import jenkins.model.JenkinsLocationConfiguration

JenkinsLocationConfiguration location = Jenkins.instance.getExtensionList('jenkins.model.JenkinsLocationConfiguration')[0]
location.url = 'https://jenkins-as-code-poc.devtail.io/'
location.save()

credentials.groovy

#!groovy

/*
 * This script loads different kinds 
 * of credentials from files into the 
 * Jenkins credential store.
 */

import jenkins.model.*
import com.cloudbees.plugins.credentials.*
import com.cloudbees.plugins.credentials.common.*
import com.cloudbees.plugins.credentials.domains.*
import com.cloudbees.plugins.credentials.impl.*
import com.cloudbees.jenkins.plugins.sshcredentials.impl.*
import org.jenkinsci.plugins.plaincredentials.*
import org.jenkinsci.plugins.plaincredentials.impl.*
import hudson.util.Secret

///////////////////
// Helper functions
///////////////////
def getStore() {
    return Jenkins.instance.getExtensionList('com.cloudbees.plugins.credentials.SystemCredentialsProvider')[0].getStore()
}

def getContent(filePath) {
    return new File(filePath).text
}

// This function reads the contents of a key file and returns
// a Jenkins SSH private key object with the given user as owner
def getSSHKeyCredential(id, path, user) {
    return new BasicSSHUserPrivateKey(
        CredentialsScope.GLOBAL,
        id,
        user,
        new BasicSSHUserPrivateKey.DirectEntryPrivateKeySource(getContent(path)),
        "",
        "SSH key ${id}"
    )
}

// Get master credential store
domain = Domain.global()

//////////////////////////////
// Add username/password pairs
//////////////////////////////
userPasswords = [
    [id: 'docker-registry', description: 'Docker Registry Credentials', userNameFile: '/var/jenkins_home/secrets/dockerUserName', userPasswordFile: '/var/jenkins_home/secrets/dockerUserPassword'],
    [id: 'github-ci-user', description: 'GitHub CI User Credentials', userNameFile: '/var/jenkins_home/secrets/githubCIUserName', userPasswordFile: '/var/jenkins_home/secrets/githubCIUserToken'], 
]

for(userPassword in userPasswords) {
    Credentials cred = (Credentials) new UsernamePasswordCredentialsImpl(CredentialsScope.GLOBAL, userPassword.id, userPassword.description, getContent(userPassword.userNameFile), getContent(userPassword.userPasswordFile))
    getStore().addCredentials(domain, cred)
}

/////////////
// Add tokens
/////////////
secretTokens = [
    [id: 'slack-token', description: 'Slack Token', tokenFile: '/var/jenkins_home/secrets/slackToken'],
    [id: 'vault-approle-secret', description: 'Vault AppRole Secret', tokenFile: '/var/jenkins_home/secrets/vaultAppRoleSecret'],
    [id: 'vault-approle-id', description: 'Vault AppRole ID', tokenFile: '/var/jenkins_home/secrets/vaultAppRoleID'],
    [id: 'github-ci-user-token', description: 'Github CI User Token', tokenFile: '/var/jenkins_home/secrets/githubCIUserToken']
]

for(secretToken in secretTokens) {
    Credentials token = (Credentials) new StringCredentialsImpl(CredentialsScope.GLOBAL, secretToken.id, secretToken.description, Secret.fromString(getContent(secretToken.tokenFile)))
    getStore().addCredentials(domain, token)
}

///////////////
// Add ssh keys
///////////////
sshKeys = [
    [id: 'ssh-deploy-key-service-a', path: '/var/jenkins_home/.ssh/deploy-key-service-a', user: 'root'],
    [id: 'ssh-slave-access', path: '/var/jenkins_home/.ssh/slave-access', user: 'jenkins'],
    [id: 'ssh-global-shared-library', path: '/var/jenkins_home/.ssh/global-shared-library', user: 'root'],
]

for(sshKey in sshKeys) {
    getStore().addCredentials(domain, getSSHKeyCredential(sshKey.id, sshKey.path, sshKey.user))
}

github.groovy

#!groovy

/*
 * This script configures the GitHub Plugin.
 * Requires the GitHub Plugin to be installed.
 * Tested with github:1.29.3
 */

import jenkins.model.Jenkins
import org.jenkinsci.plugins.github.config.GitHubPluginConfig
import org.jenkinsci.plugins.github.config.GitHubServerConfig

def githubConfig = new GitHubServerConfig("github-ci-user-token") // credential ID for our user token for the GitHub CI User
githubConfig.setManageHooks(true)
githubConfig.setName("GitHub")
def github = Jenkins.instance.getExtensionList(GitHubPluginConfig.class)[0]
github.setConfigs([
  githubConfig,
])
github.save()

githubOAuth.groovy

#!groovy

/*
 * This script configures Github OAuth access 
 * in Jenkins. It uses a global authorization 
 * Matrix strategy as authorization configurtion.
 * This script requires the Gibhub Authentication 
 * plugin (github-oauth) to be installed. It is 
 * tested with github-oauth:0.29
 */

import hudson.security.SecurityRealm
import org.jenkinsci.plugins.GithubSecurityRealm
import jenkins.model.*
import hudson.security.*

// Setup OAUTH Realm
String githubWebUri = GithubSecurityRealm.DEFAULT_WEB_URI
String githubApiUri = GithubSecurityRealm.DEFAULT_API_URI
String oauthScopes = 'read:org,user:email' //GithubSecurityRealm.DEFAULT_OAUTH_SCOPES
String clientID = System.getenv()['GITHUB_OAUTH_CLIENT_ID'] // TODO: get from credential store
String clientSecret = System.getenv()['GITHUB_OAUTH_CLIENT_SECRET'] // TODO: get from credential store

SecurityRealm github_realm = new GithubSecurityRealm(githubWebUri, githubApiUri, clientID, clientSecret, oauthScopes)
Jenkins.instance.setSecurityRealm(github_realm)

// Create global authorization matrix
def strategy = new GlobalMatrixAuthorizationStrategy()

// Give admin access to fishi0x01 user
strategy.add(Jenkins.ADMINISTER, "fishi0x01")

// Give admin access to my_team_name
strategy.add(Jenkins.ADMINISTER, "my_company_id*my_team_name")

// wrap up
Jenkins.instance.setAuthorizationStrategy(strategy)
Jenkins.instance.save()

globalEnvVars.groovy

#!groovy

/*
 * This script configures global environment variables in Jenkins
 */

import jenkins.model.Jenkins
import hudson.EnvVars;
import hudson.slaves.EnvironmentVariablesNodeProperty;
import hudson.slaves.NodeProperty;
import hudson.slaves.NodePropertyDescriptor;
import hudson.util.DescribableList;

def createGlobalEnvironmentVariables(String key, String value){

    Jenkins instance = Jenkins.getInstance();

    DescribableList<NodeProperty<?>, NodePropertyDescriptor> globalNodeProperties = instance.getGlobalNodeProperties();
    List<EnvironmentVariablesNodeProperty> envVarsNodePropertyList = globalNodeProperties.getAll(EnvironmentVariablesNodeProperty.class);

    EnvironmentVariablesNodeProperty newEnvVarsNodeProperty = null;
    EnvVars envVars = null;

    if ( envVarsNodePropertyList == null || envVarsNodePropertyList.size() == 0 ) {
        newEnvVarsNodeProperty = new hudson.slaves.EnvironmentVariablesNodeProperty();
        globalNodeProperties.add(newEnvVarsNodeProperty);
        envVars = newEnvVarsNodeProperty.getEnvVars();
    } else {
        envVars = envVarsNodePropertyList.get(0).getEnvVars();
    }
    envVars.put(key, value)
    instance.save()
}

createGlobalEnvironmentVariables('MY_ENV_VAR_A', 'A')
createGlobalEnvironmentVariables('MY_ENV_VAR_B', 'B')

globalSharedLibrary.groovy

#!groovy

/*
 * Configure pipeline shared libraries in the global Jenkins configuration.
 * This will safely compare configured libraries and only overwrite the global
 * shared library config if changes have been made.
 * workflow-cps-global-lib 2.9
 *
 * Source: https://github.com/thbkrkr/jks/blob/master/init.groovy.d/11-configure-pipeline-global-shared.groovy
 */
import jenkins.model.Jenkins
import jenkins.plugins.git.GitSCMSource
import jenkins.plugins.git.traits.BranchDiscoveryTrait
import org.jenkinsci.plugins.workflow.libs.GlobalLibraries
import org.jenkinsci.plugins.workflow.libs.LibraryConfiguration
import org.jenkinsci.plugins.workflow.libs.SCMSourceRetriever

List libraries = [] as ArrayList

def remote = 'git@github.com:<my-org>/<my-shared-library>.git'
def credentialsId = 'ssh-global-shared-library'

name = 'lib-name'
defaultVersion = 'master'

if (remote != null) {

    def scm = new GitSCMSource(remote)
    if (credentialsId != null) {
        scm.credentialsId = credentialsId
    }

    scm.traits = [new BranchDiscoveryTrait()]
    def retriever = new SCMSourceRetriever(scm)

    def library = new LibraryConfiguration(name, retriever)
    library.defaultVersion = defaultVersion
    library.implicit = false
    library.allowVersionOverride = true
    library.includeInChangesets = false

    libraries << library

    def global_settings = Jenkins.instance.getExtensionList(GlobalLibraries.class)[0]
    global_settings.libraries = libraries
    global_settings.save()
    println 'Configured Pipeline Global Shared Libraries:\n    ' + global_settings.libraries.collect { it.name }.join('\n    ')
}

init.groovy

#!groovy

/*
 * This script is designated for the init.groovy.d 
 * directory to be executed at startup time of the 
 * Jenkins instance. This script requires the jobDSL
 * Plugin. Tested with job-dsl:1.70
 */

import javaposse.jobdsl.dsl.DslScriptLoader
import javaposse.jobdsl.plugin.JenkinsJobManagement
import jenkins.model.Jenkins
import com.cloudbees.plugins.credentials.domains.Domain
import com.cloudbees.jenkins.plugins.sshcredentials.impl.BasicSSHUserPrivateKey
import com.cloudbees.plugins.credentials.CredentialsScope
import hudson.security.FullControlOnceLoggedInAuthorizationStrategy
import hudson.security.HudsonPrivateSecurityRealm

// Add deploy key for the centrally shared pipeline and configuration repository
def domain = Domain.global()
def store = Jenkins.instance.getExtensionList('com.cloudbees.plugins.credentials.SystemCredentialsProvider')[0].getStore()
def keyFileContents = new File("/var/jenkins_home/.ssh/shared-libraries-deploy-key").text
def privateKey = new BasicSSHUserPrivateKey(
  CredentialsScope.GLOBAL,
  "shared-libraries-deploy-key",
  "root",
  new BasicSSHUserPrivateKey.DirectEntryPrivateKeySource(keyFileContents),
  "",
  "SSH key for shared-library"
)
store.addCredentials(domain, privateKey)

// Create the configuration job interface from a jobDSL script
def jobDslScript = new File('/var/jenkins_home/init-dsl/ConfigurationAndSeedingPipelineDSL.groovy')
def workspace = new File('.')
def jobManagement = new JenkinsJobManagement(System.out, [:], workspace)
new DslScriptLoader(jobManagement).runScript(jobDslScript.text)

// Disable Setup Wizards
if(Jenkins.instance.getSecurityRealm().getClass().getSimpleName() == 'None') {
    def instance = Jenkins.getInstance()
  
    // Those files should be mounted into the jenkins master container
    def setupUser = new File("/var/jenkins_home/jenkins-basic-auth-credentials/default-setup-user").text.trim()
    def setupPass = new File("/var/jenkins_home/jenkins-basic-auth-credentials/default-setup-password").text.trim()

    def hudsonRealm = new HudsonPrivateSecurityRealm(false)
    instance.setSecurityRealm(hudsonRealm)
    def user = instance.getSecurityRealm().createAccount(setupUser, setupPass)
    user.save()

    def strategy = new FullControlOnceLoggedInAuthorizationStrategy()
    strategy.setAllowAnonymousRead(false)
    instance.setAuthorizationStrategy(strategy)

    instance.save()

    println("SetupWizard Disabled")
}

maven.groovy

#!groovy

/*
 * This script makes the maven tool available on all Jenkins nodes.
 * Requires the maven plugin to be installed.
 */

import hudson.tasks.Maven.MavenInstallation;
import hudson.tools.InstallSourceProperty;
import hudson.tools.ToolProperty;
import hudson.tools.ToolPropertyDescriptor;
import hudson.util.DescribableList;

// Install maven tool
def mavenDesc = jenkins.model.Jenkins.instance.getExtensionList(hudson.tasks.Maven.DescriptorImpl.class)[0]

def isp = new InstallSourceProperty()
def autoInstaller = new hudson.tasks.Maven.MavenInstaller("3.3.9")
isp.installers.add(autoInstaller)

def proplist = new DescribableList<ToolProperty<?>, ToolPropertyDescriptor>()
proplist.add(isp)

def installation = new MavenInstallation("M3", "", proplist)

mavenDesc.setInstallations(installation)
mavenDesc.save()

slack.groovy

#!groovy

/*
 * This script configures the Jenkins Slack Plugin.
 * Requires the installation of the Slack Plugin.
 * Tested with slack:2.3
 */

import jenkins.model.Jenkins

def slack = Jenkins.instance.getExtensionList('jenkins.plugins.slack.SlackNotifier$DescriptorImpl')[0]
slack.tokenCredentialId = 'slack-token'
slack.teamDomain = 'my-slack-team-domain'
slack.baseUrl = 'https://my-slack-team-domain.slack.com/services/hooks/jenkins-ci/'
slack.save()

slaves.groovy

#!groovy

import jenkins.model.*
import hudson.model.*
import hudson.slaves.*
import hudson.plugins.sshslaves.*
import java.util.ArrayList;
import hudson.slaves.EnvironmentVariablesNodeProperty.Entry;

// Prepare env vars for slave node
List<Entry> env = new ArrayList<Entry>();
env.add(new Entry("key1","value1"))
env.add(new Entry("key2","value2"))
EnvironmentVariablesNodeProperty envPro = new EnvironmentVariablesNodeProperty(env);

// Define slave to be bootstrapped by master
Slave slave = new DumbSlave(
    "my-slave-id",
    "My slave description",
    "/path/to/slave/workdir",
    "4", // # of executors
    Node.Mode.EXCLUSIVE,
    "slave-label",
    new SSHLauncher(System.getenv()['MY_SLAVE_ADDRESS'], 22, SSHLauncher.lookupSystemCredentials("my-slave-ssh-key-credential-id"), "", null, null, "", "", 60, 3, 15),
    new RetentionStrategy.Always(),
    new LinkedList()
)

// Add env vars to slave
slave.getNodeProperties().add(envPro)

// Save slave
Jenkins.instance.addNode(slave)

sshd.groovy

#!groovy

/*
 * This script configures the Jenkins SSHD Port.
 */

import jenkins.model.Jenkins

def sshDesc = Jenkins.instance.getDescriptor("org.jenkinsci.main.modules.sshd.SSHD")
sshDesc.setPort(6666)
sshDesc.getActualPort()
sshDesc.save()

theme.groovy

#!groovy

/*
 * This script configures the simple theme plugin.
 * Requires the simple theme plugin to be installed.
 * Tested with simple-theme-plugin:0.5.1
 *
 * Use http://afonsof.com/jenkins-material-theme/ to generate a new jenkins theme.
 * Upload the theme to a CDN or place it directly at the userContent directory of 
 * Jenkins to be publicly available.
 */

import jenkins.model.Jenkins
import org.jenkinsci.plugins.simpletheme.CssUrlThemeElement


def themeDecorator = Jenkins.instance.getExtensionList(org.codefirst.SimpleThemeDecorator.class).first()

themeDecorator.setElements([
  new CssUrlThemeElement('https://fishi.devtail.io/content-images/jenkins-devtail-theme.css')
])

Jenkins.instance.save()

timezone.groovy

#! groovy

/*
 * This script configures the timezone in Jenkins
 */

System.setProperty('org.apache.commons.jelly.tags.fmt.timeZone', 'Europe/Berlin')

triggerConfigurationAsCodePlugin.groovy

#! groovy

import jenkins.model.Jenkins

// trigger configuration as code plugin
def jcacPlugin = Jenkins.instance.getExtensionList(io.jenkins.plugins.casc.ConfigurationAsCode.class).first()
jcacPlugin.configure()

userPublicKeys.groovy

#! groovy

def getFileContent(filePath) {
    return new File(filePath).text
}

def user = hudson.model.User.get('admin')

def pubKey = new org.jenkinsci.main.modules.cli.auth.ssh.UserPropertyImpl(getFileContent('/var/jenkins_home/jenkins-ssh-keys/ssh-jenkins-cli.pub'))
user.addProperty(pubKey)

user.save()