BIRCH BIRCH - Adding locally-installed programs and documentation

Goal: To add programs or documentation to the local BIRCH installation in such a way that the users cannot distinguish what is in the BIRCH core from what has been added locally.

Summary: For binaries, this is accomplished simply by adding programs to already-existing local/bin or local/script directories. To launch locally-installed  programs from bioLegato, you can add menu items to the the appropriate bioLegato directory in local/dat. These include:
The new menu items are merged into the BIRCH core bioLegato menus automatically when a bioLegato instance launches. For documentation, we need to add paths and descriptions of the documentation to the local copy of the birchdb database. The script merges local and BIRCH core documentation into a single set of web pages. Remember: all of these changes are automatically merged into BIRCH each time you update BIRCH.

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