Integrate bundle help files with core help

[Greg Couch]

Start by modifying help URLs to work with help in bundles: help:user/commands/cmd_name.html would look in the bundle for cmd_name.html. Likewise for help:user/tool/tool_name.html. Others? help:user/format/format_name.html?

Autogenerate list of all commands? Combined search index? Could have combined list when downloading list of all bundles, and go to ChimeraX Toolshed website for uninstalled tools.

[pett]

Milestone renamed

[Greg Couch]

Done. User manual index is automatically augmented with additional tools and commands. Bundles, whose documentation is independent of the core, should have a docs/tools/tool_name.html file and/or a docs/user/commands/command.html file included in the bundle (see the tut_gui and tut_cmd examples).