Include transitive file dependencies during Gradle repackaging

Previously, ProjectLibraries only considered a configuration's
direct file dependencies. This meant that a transitive file
dependency that should have been pulled in via a project dependency
was not included in the repackaged jar's lib directory.

ProjectLibraries has been updated to walk down the tree of project
dependencies and create libraries for any file dependencies that
are found.

Fixes gh-1368
Merge branch '1.1.x'
Add jar that should have been added as part of 69c61d0
Preserve JVM args when auto-configuring a Java agent in Gradle bootRun

Fixes #1411
Merge branch '1.1.x'
Align MessageSource path search fix with SPR-12095

Update ExtendedPathMatchingResourcePatternResolver to use similar
code as the fix for SPR-12095.

Fixes gh-1378
Fix InteliJ code formatter instructions

Update CONTRIBUTING.adoc with improved code formatter instructions.

Fixes gh-1271
Merge branch '1.1.x'
Fix asciidoc incorrect link syntax
Merge branch '1.1.x'
Use org.hsqldb.jdbc.JDBCDriver HSQLDB Driver

Switch driver class to the more conventionally named
`org.hsqldb.jdbc.JDBCDriver`.
Polish spaces->tabs
Relocate configuration prefix constant

Relocate DataSourceAutoConfiguration.CONFIGURATION_PREFIX to
DataSourceProperties.PREFIX.
Polish
Detect embedded DBs when deducing driver class

Fix DataSourceProperties getUsername() and getPassword() methods to
call getDriverClassName() rather than using `this.driverClassName` to
ensure than deduced driver classes can be used.

Fixes gh-1421
Merge branch '1.1.x'
Add activemq-jms-pool managed dependency

Fixes gh-1423
Merge branch '1.1.x'

Conflicts:
	spring-boot-dependencies/pom.xml
Restore repositories section

Restore repositories section accidentally removed during the merge
Revert "Add activemq-jms-pool managed dependency"

This reverts commit bbdfcd4faa9451b656b9f156b53dd40333c3324b.