To compile and package a new version, follow these steps:

1a. Clone bioformats and change into the repos directoryh:
$ git clone git://github.com/openmicroscopy/bioformats.git
$ cd bioformats

1b. ... or pull the latest changes:
$ cd bioformats
$ git pull 

2. Checkout the version you want to build (see 'git tag' for which tags are available). As of the time of this writing, v4.4.6 is the current release version:
$ git checkout v4.4.6

3. Cherry pick commits listed in patches.txt.
$ git cherry-pick ff038535ff26f1c94c0f67b69229f212edf963b0
(...)

If the commits that you want to cherry pick are already in the version you want to upgrade to - you can remove them from the patches.txt file.

4. Copy the packaging script 'create_openbis_bioformats.sh' from the libraries/bioformats directory into the bioformats git directory:
$ cp ~/dev/workspace_openbis/libraries/bioformats/create_openbis_bioformats.sh .

5. Run the script:
$ ./create_openbis_bioformats.sh

6. Copy the files bioformats.jar and bioformats_src.zip back into the libraries/bioformats directory and update the version.txt file accordingly.

Note: the create_openbis_bioformats.sh repackages the classes produced by the bioformats ant script. What classes need to be added may change over time. So if you build a new major version, you need to check that all relevant files have been packaged into bioformats.jar!