org.eclipse.jgit/src/org/eclipse/jgit/diff/MyersDiff.java (12 lines):
	- line 121: // TODO: use ThreadLocal for future multi-threaded operations
	- line 211: // TODO: measure speed impact when this is synchronized
	- line 283: int minK, maxK; // TODO: better explanation
	- line 286: // TODO: remove
	- line 293: // TODO: remove
	- line 300: // TODO: remove
	- line 373: // TODO: handle i more efficiently
	- line 374: // TODO: walk snake(k, getX(d, k)) only once per (d, k)
	- line 375: // TODO: move end points out of the loop to avoid conditionals inside the loop
	- line 383: // TODO: refactor into its own function
	- line 467: // TODO: move out of loop
	- line 515: // TODO: move out of loop


org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/GC.java (7 lines):
	- line 284: // TODO: implement reflog_expire(pm, repo);
	- line 287: // TODO: implement rerere_gc(pm);
	- line 764: // TODO: abstract this more cleanly.
	- line 887: // TODO: the exception has to be wrapped into an IOException because
	- line 894: // TODO: abstract this more cleanly.
	- line 1658: // TODO run pre-auto-gc hook, if it fails return false
	- line 1663: // TODO: if JGit GC is enhanced to support repack's option -l this


org.eclipse.jgit/src/org/eclipse/jgit/dircache/DirCacheCheckout.java (5 lines):
	- line 729: // TODO: check whether it is always correct to report a conflict here
	- line 829: // TODO: make use of tree extension as soon as available in jgit
	- line 1139: // TODO check that we don't overwrite some unsaved
	- line 1300: // TODO: couldn't we delete unsaved worktree content here?
	- line 1703: // TODO: wire correctly with AUTOCRLF


org.eclipse.jgit.gpg.bc/src/org/eclipse/jgit/gpg/bc/internal/keys/SExprParser.java (3 lines):
	- line 218: // TODO: type of RSA key?
	- line 357: // TODO: type of RSA key?
	- line 422: // TODO: recognise other algorithms


org.eclipse.jgit/src/org/eclipse/jgit/transport/WalkEncryption.java (3 lines):
	- line 61: // TODO mixed ciphers
	- line 193: // TODO back port this change to JetS3t V2
	- line 409: // TODO re-factor AmazonS3.putImpl to be more transaction-like


org.eclipse.jgit/src/org/eclipse/jgit/api/ResetCommand.java (3 lines):
	- line 79: MERGE, // TODO not implemented yet
	- line 85: KEEP // TODO not implemented yet
	- line 136: // @TODO throw an InvalidRefNameException. We can't do that


org.eclipse.jgit/src/org/eclipse/jgit/lib/Repository.java (2 lines):
	- line 205: * TODO This method should be annotated as Nullable, because in some
	- line 287: * TODO This method should be annotated as Nullable, because in some


org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsRefRename.java (2 lines):
	- line 28: // TODO Correctly handle renaming foo/bar to foo.
	- line 29: // TODO Batch these together into one log update.


org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/JGitUserInteraction.java (2 lines):
	- line 87: // TODO Possibly change EGit to store all hidden strings
	- line 138: // TODO Implement password update in password authentication?


org.eclipse.jgit/src/org/eclipse/jgit/api/RebaseCommand.java (2 lines):
	- line 121: private static final String GIT_REBASE_TODO = "git-rebase-todo"; //$NON-NLS-1$
	- line 545: // TODO if the content of this commit is already merged


org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/OpenSshServerKeyDatabase.java (2 lines):
	- line 127: // TODO: GlobalKnownHostsFile? May need some kind of LRU caching; these
	- line 245: // TODO: OpenSsh disables password and keyboard-interactive


org.eclipse.jgit/src/org/eclipse/jgit/transport/BasePackConnection.java (1 line):
	- line 360: // TODO: for now we only do protocol V2 for fetch. For push


org.eclipse.jgit/src/org/eclipse/jgit/api/CheckoutCommand.java (1 line):
	- line 201: // TODO Git CLI supports checkout from unborn branch, we should


org.eclipse.jgit/src/org/eclipse/jgit/internal/diffmergetool/FileElement.java (1 line):
	- line 226: // TODO: avoid long random file name (number generated by


org.eclipse.jgit/src/org/eclipse/jgit/api/AddCommand.java (1 line):
	- line 205: // inserting. TODO: Fix this by using Buffers.


org.eclipse.jgit/src/org/eclipse/jgit/transport/ReceivePack.java (1 line):
	- line 1876: // TODO: Using get/setMessage to store an OID is a


org.eclipse.jgit/src/org/eclipse/jgit/api/ArchiveCommand.java (1 line):
	- line 244: * TODO: check that suffixes don't overlap.


org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsConfig.java (1 line):
	- line 34: // TODO actually store this configuration.


org.eclipse.jgit/src/org/eclipse/jgit/merge/ResolveMerger.java (1 line):
	- line 1801: * TODO: enhance WorkingTreeIterator to support write operations. Then this


org.eclipse.jgit/src/org/eclipse/jgit/util/FileUtils.java (1 line):
	- line 1010: // TODO: Would it be faster to check with isNormalized first


org.eclipse.jgit/src/org/eclipse/jgit/transport/ProtocolV0Parser.java (1 line):
	- line 109: // TODO: timestamps should be long


org.eclipse.jgit/src/org/eclipse/jgit/diff/DiffFormatter.java (1 line):
	- line 583: // TODO: consider propagating once bug 536323 is tackled


org.eclipse.jgit/src/org/eclipse/jgit/api/StashApplyCommand.java (1 line):
	- line 388: // TODO maybe NameConflictTreeWalk ?


org.eclipse.jgit/src/org/eclipse/jgit/patch/PatchApplier.java (1 line):
	- line 309: // TODO: it would be nice if we could return a TreeWalk at EOF


org.eclipse.jgit.http.apache/src/org/eclipse/jgit/transport/http/apache/HttpClientConnection.java (1 line):
	- line 407: // TODO: check whether we can really ignore this.


org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/dfs/DfsRepository.java (1 line):
	- line 123: // TODO Check if the implementation used in FileRepository can be used


org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/AuthenticationLogger.java (1 line):
	- line 219: // TODO: keyboard-interactive? sshd 2.8.0 has no callback


org.eclipse.jgit.ssh.apache/src/org/eclipse/jgit/internal/transport/sshd/JGitPublicKeyAuthentication.java (1 line):
	- line 108: // TODO: remove this once we're on an sshd version that has SSHD-1272


org.eclipse.jgit/src/org/eclipse/jgit/api/CloneCommand.java (1 line):
	- line 378: return; // TODO throw exception?


org.eclipse.jgit/src/org/eclipse/jgit/api/DescribeCommand.java (1 line):
	- line 424: // TODO: if all the commits in the queue of RevWalk has allFlags


org.eclipse.jgit.http.apache/src/org/eclipse/jgit/transport/http/apache/TemporaryBufferEntity.java (1 line):
	- line 73: // TODO: dont we need a progressmonitor


org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/DiffTool.java (1 line):
	- line 245: // TODO: check how to return the exit-code of the tool


org.eclipse.jgit/src/org/eclipse/jgit/internal/storage/file/FileRepository.java (1 line):
	- line 535: // TODO: use exactRef here, which offers more predictable and therefore preferable


org.eclipse.jgit.lfs.server/src/org/eclipse/jgit/lfs/server/fs/ObjectUploadListener.java (1 line):
	- line 164: // TODO check if status 200 is ok for PUT request, HTTP foresees 204


org.eclipse.jgit.pgm/src/org/eclipse/jgit/pgm/MergeTool.java (1 line):
	- line 284: // TODO: check how to return the exit-code of the