IJ2 is out
 Sec. 25: Customizing the IJ Interface Up Main page Sec. 26: File

Part V. Menu Commands

As described in ImageJ User Interface↑, the menu bar lists all ImageJ commands. It is organized in eight menus:
File Basic file operations (opening, saving, creating new images). Most are self-explanatory.
Edit Editing and drawing operations as well as global settings.
Image Conversion and modification of images including geometric transformations.
Process Image processing, including point operations, filters and arithmetic operations.
Analyze Statistical measurements, profile and histogram plotting and other operations related to image analysis.
Plugins Commands for creating, editing and managing add-ons (see Extending ImageJ↑), listing all the user-installed Macros↑, Scripts↑ and Plugins↑ installed in the ImageJ/plugins/ directory.
Window Selection and management of open windows.
Help Updates, documentation resources and version information.
8 Organizing Commands in the Menu Bar
The Plugins menu can become easily cluttered after the installation of several plugins. Since Plugins reflects the hierarchy of directories in ImageJ/plugins/ (up to two subfolders), submenus (i.e., subfolders) can be created to keep the menu organized, preventing it from running off the bottom of the screen. E.g, to move the EPS Writer plugin into a PluginsInput-OutputPDF submenu, one would move EPS_Writer.class into ImageJ/plugins/Input-Output/PDF/.
In addition, checking the Move isolated plugins to Misc. menu checkbox in EditOptionsMisc…↓ will compact the menu list by moving to PluginsMiscellaneous all the plugins with only one command that try to install themselves in submenus.
Note that external plugins can be installed in any of the ImageJ menus. This is the case of plugins packaged in JAR files containing a configuration file (plugins.config) specifying the location of the new commands implemented by the plugin. You can rename, reorganize or move commands implemented by external plugins by editing their plugins.config file as described on the JAR demo documentation page. If you don’t know in which menu a plugin has been registered, use Show full information in the command Finder (PluginsUtilitiesFind Commands… [l]↓) to find out the location of the installed .jar files.
With Fiji↑, Scripts↑ and Macros↑ can be registered in any menu by saving into Fiji.app/plugins/Scripts/menu name/submenu name/. E.g., a certain macro (.ijm file) saved in Fiji.app/plugins/Scripts/File/Import/ is registered in the FileImport submenu.
ImageJ's plugin architecture on the Fiji website
 Sec. 25: Customizing the IJ Interface Up Main page Sec. 26: File