* Implement ours/theirs content conflict resolution

* Fix formatting of config option values

* Export new package org.eclipse.jgit.logging and import it where used

* Merge branch 'stable-5.5'

* Merge branch 'stable-5.2' into stable-5.3

* BitmapCalculator: javadoc fixes

* ReachabilityCheckers: @since 5.4
* Update Orbit to S20190521195709 for 2019-06 M3
* Tune max heap size for tests

* Revert 4678f4b and provide another solution for bug 467631

* Fix pack files scan when filesnapshot isn't modified

* pgm: Fix missing braces in Push.run()
* pgm: Handle exceptions in Push command
* pgm: Fix missing braces in MergeBase.run()
* pgm: Handle IOException in MergeBase command
* pgm: Fix missing braces in Merge command
* pgm: Handle exceptions in Merge command
* pgm: Fix missing braces in LsTree.run()
* pgm: Handle exceptions in LsTree command
* pgm: Fix missing braces in LsRemote.run()
* pgm: Handle exceptions in LsRemote command
* pgm: Handle exceptions in LsFiles command
* pgm: Fix missing braces in Log.run()
* pgm: Handle exceptions in Log command
* pgm: Handle exceptions in Init command
* pgm: Handle IOException in IndexPack command
* pgm: Fix missing braces in Fetch.run()
* pgm: Handle IOException in Fetch command
* pgm: Handle GitAPIException in Gc command
* pgm: Fix missing braces in DiffTree.run()
* pgm: Handle exceptions in DiffTree command

* Merge branch 'stable-5.0'

* Temporarily @Ignore flaky CommitCommandTest methods

* AmazonS3: Open OutputStream in try-with-resource
* MergeGitAttributeTest: Open FileInputStream in try-with-resource
* PullCommandWithRebaseTest: Open File{Input|Output}Stream in try-with-resource
* RecursiveMergerTest: Open FileOutputStream in try-with-resource

* Fix JGit set core.fileMode to false by default instead of true for non Windows OS.

* Improve BatchRefUpdateTest readability
* Move BatchRefUpdate tests to a new file
* Implement atomic BatchRefUpdates for RefDirectory
* Separate RefUpdate.Result.REJECTED_{MISSING_OBJECT,OTHER_REASON}

* Skip javadoc generation for org.eclipse.jgit.http.test

* [infer] Fix resource leaks in RebaseCommand
* [infer] Fix resource leak in BlameCommand

* Deprecate SafeBufferedOutputStream

* Fix TransportException when reading bundle

* BaseRepositoryBuilder should trim CR from .git symref

* PushCertificateParser: Move reader parsing to instance method
* PushCertificateParser: Make constructor public
* Report PackProtocolExceptions to client during receive-pack
* PushCertificate: implement hashCode/equals/toString
* PushCertificateParser: Make pushee optional
* PushCertificateParser: Change error string for invalid field
* PushCertificateParser: Add method for parsing from a stream
* IO: Add a method for reading lines
* BaseReceivePack: Treat all LFs as optional
* BaseReceivePack: More validation during parseCommand

* TestRepository: Allow setting explicit Change-Id
* TestRepository: Ignore existing Change-Id in message
* TestRepository: Support committing to unborn symref
* TestRepository: Expose some getters for CommitBuilder
* TestRepository: Add methods to amend commits or refs
* TestRepository: Add a reset method to move HEAD around
* TestRepository: Optionally insert Change-Id in commit message

* Merge branch 'stable-3.4'

* Add missing space to invalid object error messages

* Fix line endings and whitespace errors in jgit feature

* Remove packIndex field from FileObjDatabase openPack method.
* Update DfsObjDatabase API to open/write by pack extension.

* TemporaryBuffer: Fix reading from in-memory InputStream