Overview of Fiji's source codeshort URL
This page will give you an idea how Fiji's source code is organized. Every directory referred to is relative to the Fiji root, i.e. the directory into which you cloned fiji.git.
The Fiji launcher
The whole purpose of the launcher is to make launching Java and Fiji easier, but there are a few other niceties in there, such as running Jython scripts or .jar files with the same classpath as Fiji.
The generated launcher is <Fiji-root>/fiji (or on Windows, fiji.exe).
We try to avoid plugins without sources, but even those are not tracked in <Fiji-root>/plugins/, but rather in <Fiji-root>/staged-plugins. The reason is that we would want to provide our very own plugins.config files with them, i.e. we want to have custom locations/names of the plugins contained in the .jar file.
Such plugins.config files that are to be inserted in certain .jar also live in staged-plugins, as <basename-of-jar>.config. Example: the plugins.config for loci_tools.jar is stored in <Fiji-root>/staged-plugins/loci_tools.config.
The sources for many plugins shipped with (and maintained in) Fiji live in <Fiji-root>/src-plugins. The subdirectories in src-plugins mostly correspond to the basename of the .jar file generated from it. Example: the sources of plugins/Fiji_Updater.jar are stored in <Fiji-root>/src-plugins/Fiji_Updater/.
Some plugins require third-party libraries such as Jama. Such libraries are not stored in plugins/ (lest an underscore in their filenames would make ImageJ mistake them for plugins), but in jars/ instead.
Some of the libraries' sources are stored in src-plugins/ (in subdirectories corresponding to the basename of the respective .jar file).
Some components of Fiji are stored in submodules, i.e. in Git repositories of their own right. This is the case for ImageJA, many third-party libraries, and some plugins collections that existed before Fiji, such as TrakEM2 or Bio-Formats.
These submodules are subdirectories in <Fiji-root>/modules/, and they may, or may not, be checked out.
Every submodule is "committed" at a certain revision, i.e. Git not only records where, say, ImageJA is to be cloned from, but also what revision is current for any given commit in fiji.git.
If submodules are checked out, you can cd into the respective directories and work with them as with other Git repositories.
Our policy, however, is that you do not need to check out the submodules if you do not want to work on them: the result of the most recently committed revision needs to be committed as binary in <Fiji-root>/precompiled/. For example, the .jar file generated from the bio-formats submodule is committed as precompiled/loci_tools.jar.
The Fiji Build system
For historical reasons, the Fiji Build system's source code lives in <Fiji-root>/fake/Fake.java. It will be compiled into <Fiji-root>/fake.jar.
To avoid a chicken-and-egg problem, a fake.jar that can compile the current Fiji Build system is committed to precompiled/ (and for the same reason, precompiled versions of the Fiji launchers for all supported platforms live there, too).
The precompiled/ directory
Precompiled versions of all .jar files generated from submodules, of fake.jar and of the Fiji launchers live in precompiled/.
The bin/ directory
Quite a few tasks -- such as committing a new submodule or sources for a plugin, or releasing a new version of Fiji -- are performed by scripts. These scripts live in the <Fiji-root>/bin/ subdirectory.
Some of these scripts are shell scripts, others are Jython scripts with special shebang lines which trigger them to be called with the current Fiji launcher.
The nightly-build/ directory
We have a cronjob that builds Fiji every night, from then-current sources. The responsible script is bin/nightly-build.sh.
Of course, it might often be quite handy to do the same locally, i.e. compile from a completely pristine state (e.g. to ensure that your latest commit includes all necessary files). You can easily do that by calling ./bin/nightly-build.sh HEAD, which will automatically create an appropriate nightly-build/ subdirectory (if it does not exist yet), and simulate a from-scratch build.