Closes gh-5046

Closes gh-6417

Update Log4J2LoggingSystem so that the FILTER is applied to the main
configuration and not to the root logger. Prior to this commit calls
to `logger.isErrorEnabled()` would not consider the filter and hence
would always return `true`. This caused `SpringApplication` to silently
swallow exceptions.

Fixes gh-5271

Closes gh-6415

Fixes gh-6387

Closes gh-6339

Previously, one SpringApplicationAdminMXBeanRegistrar was created
per context. When there was more then one context this would result
in a javax.management.InstanceAlreadyExistsException being thrown
as an attempt was made to register the MBean more than once.

This commit updates SpringApplicationAdminJmxAutoConfiguration so
that the registrar is only created when there's no such existing bean
in the context hierarchy.

Closes gh-6378

* gh-6381:
  Upgrade to Thymeleaf 2.1.5.RELEASE

Closes gh-6381

Previously, if there was a hierarchy of SpringApplications, the admin
MBean would report that the application was ready as soon as any
application in the hierarchy was ready. This could lead to a client
trying to query a property in the environment before it's available.

This commit updates the MBean registrar to that the MBean only reports
that the application is ready when the context that contains the
registrar has refreshed and fired its ApplicationReadyEvent.

Closes gh-6362

Closes gh-6360

Previously, the shutdown endpoint would spawn a new thread to perform
the shutdown but did not explicitly configure its thread context
class loader (TCCL). This mean that the new thread would use the
request thread's TCCL as its TCCL. This meant that a different TCCL
would be used compared to a shutdown triggered by the shutdown hook
and also caused problems with Tomcat's thread leak detection logic.

This commit updates the shutdown endpoint to explicitly configure the
TCCL of the shutdown thread to be the ClassLoader that loaded the
endpoint's class.

Closes gh-6361

Closes gh-6358

Closes gh-6344

Commit 3ea84f9e has wrongly introduced a `@Primary` marker on
`IntegrationMBeanExporter` so any use of both Spring's JMX support
and Spring Integration's JMX support leads to an exception. This commit
makes sure to remove the unnecessary `@Primary`

Closes gh-6328

Closes gh-6249

Closes gh-6315

Fixes gh-6312

Closes gh-6275

Closes gh-6276

Closes gh-6276

Closes gh-6274

Closes gh-6273

Closes gh-6271

Closes gh-6270

Closes gh-6269

Closes gh-6268

Closes gh-6267

Closes gh-6266

Closes gh-6265

Previously, Log4J2LoggingSystem used ResourceUtils.isFileURL(URL) to
check that the URL of the configuration was suitable for accessing as a
File. Unfortunately, this fails when the URL’s protocol is vfs or
vfsfile as both return true and then fail when the URL is subsequently
passed into ResourceUtils.getFile(URL).

This commit switches to checking that the URL’s protocol is file,
the only protocol that will allow getFile(URL) to succeed.

Closes gh-6246

Closes gh-6245

See gh-6249

* pr/6176:
  Polish "Use missing MongoClientOptions in MongoProperties"
  Use missing MongoClientOptions in MongoProperties

Closes gh-6176