Closes gh-13917

Closes gh-13906

Closes gh-13883

See gh-13917

Co-authored-by: Andy Bell <andyrbell@gmail.com>

Closes gh-13863

* gh-13818:
  Add null guards for getBeanDefinition() in BeanTypeRegistry

Closes gh-13818

Closes gh-13839

Closes gh-13838

Closes gh-13807

Closes gh-13803

* pr/13792:
  Add missing @Test in RestarterTests

Closes gh-13792

* pr/13779:
  Remove carriage returns in TypeUtils.getJavaDoc()

Closes gh-13779

Closes gh-13601

* pr/13755:
  Fix typo

Closes gh-13755

Previously, when a bean was overridden and its type changes,
BeanTypeRegistry could be left with a stale view of the bean's type.
This would lead to incorrect bean condition evaluation as conditions
would match or not match based on the bean's old type.

This commit updates the type registry to refresh its view of a bean's
type when its definition changes.

Closes gh-13588

Previously, the initialization of StandardServletEnvironment's
property sources in SpringBootServletInitializer led to debug logging
calls being made before the LoggingSystem had been initialized. As a
result, the system's default configuration was used and, in the case
of Logback at least, the debug logging was output to System.out
in a war deployment.

This commit updates SpringBootServletInitializer to delay the
initialization of StandardServletEnvironment's property sources until
after the LoggingSystem has been initialized, but still in time for
active profiles to be configured via servlet context parameters
(see gh-9972).

Closes gh-13736

During processing of a configuration class, the class's complete
hierarchy is processed and during the processing of each class its
member classes are processed. Previously, each pool-specific
inner-class of DataSourceConfiguration extended the abstract outer
class. This meant that when the import from
DataSourceAutoConfiguration.PooledDataSourceConfiguration caused the
first pool-specific inner-class to be  processed,
DataSourceConfiguration would be processed as it was the inner-class's
superclass. In turn all of DataSourceConfiguration's member classes
would then be processed. This caused the first import (of
DataSourceConfiguration.Tomcat) to trigger processing of all of the
other pool-specific inner-classes in whatever order they were found
rather than them being processed in the order in which they are
imported by DataSourceAutoConfiguration.PooledDataSourceConfiguration.

Another part of the problem was that none of the pool-specific
inner-classes were conditional on a missing DataSource bean. This
meant that, when multiple pools were on the classpath, each class
after the first would override the previous class's definition of the
DataSource bean.

This commit updates each of the pool-specific inner-classes so that
they no longer extend DataSourceConfiguration. This ensures that
the inner classes are processed in the order defined in the import
on PooledDataSourceConfiguration. Each of the classes has also been
annotated with @ConditionalOnMissingBean(DataSource.class). This
prevents the DataSource bean definition from being overridden and
ensures that the order of precedence for the pool that will be used
is as defined in the import.

Closes gh-13737

Previously, if a jar that used custom compression configuration was
repackaged, a failure may occur if an entry in the repackaged jar had
a different compressed size to the entry in the source jar.

This commit updates JarWriter to clear the input entry's compressed
size (by setting it to -1) so that the repackaged entry's compressed
size does not have to match that of the input entry.

Closes gh-13720

Closes gh-13709

Closes gh-13640

Closes gh-13639

Closes gh-13638

Closes gh-13637

Closes gh-13607

Closes gh-13551

* gh-13559:
  Polish “Close Database to reset Connection's auto commit property”
  Close Database to reset Connection's auto commit property

Closes gh-13559

Previously, LiquibaseEndpoint closed the JdbcConnection but did not
close the Database. When using a connection pool, this could leave the
underlying SQL Connection with its auto commit property set to false.

This commit updates LiquibaseEndpoint to close the Database. This
ensures that it resets that Connection's auto commit property to the
value that it had when the Database was configured to use the
Connection.

See gh-13559