web/BIEN3/Redmine/svn-web/.htaccess: use Redmine/ instead of main/ subdir
schemas/VegBIEN/: moved Redmine/, TWiki/ to web/BIEN3/ since they relate to the BIEN3 project as a whole, not just the database
merged inputs/VegBIEN into schemas/VegBIEN, since for the purposes of the data dictionary URLs, VegBIEN is primarily an exchange schema
moved everything into /trunk/ to create the standard svn layout, for use with tools that require this (eg. git-svn). IMPORTANT: do NOT do an `svn up`. instead, re-use your working copy's existing files with `svn switch` (http://svnbook.red-bean.com/en/1.6/svn.ref.svn.c.switch.html).
web/**/.htaccess: RewriteRules: ensured flags are in alphabetical order
web/**/.htaccess: Use [qsappend] flag with all RewriteRules to ensure that the original query string is never lost
web/**/.htaccess: Removed preprocessing commands that need to run for every dir, because these are now inherited from the outermost .htaccess using InheritBefore. This allows the inner .htaccess files to focus just on the fallback rewrites, without needing lots of boilerplate code (except for the obligatory RewriteEngine/RewriteOptions/SetEnvIf preamble).
web/**/.htaccess: Use InheritBefore RewriteOption so that the outermost dir's rules are always run first. This is necessary so that all the HTTP_HOST and dotpath handlers, etc. are applied before any fallback handlers, without needing to copy and paste each rule into every .htaccess file. (Note that the InheritBefore RewriteOption is only available in Apache 2.4.) The outermost .htaccess file, however, must not use InheritBefore because this would inherit rules from the global Apache config, which normally should not be run and which cause an infinite redirect loop.
web/**/.htaccess: fallback rules which should not be inherited by subdirs: Filter using a RewriteCond on %{ENV:innermost_dir} so that the rule is only run if the innermost dir was this dir. (This is needed when using InheritBefore.)
web/**/.htaccess: Added SetEnvIf directives to set the $innermost_dir env var, which is used by InheritBefore RewriteRule inheritance. You can easily populate the current dir name in jEdit by right-clicking the buffer tab and selecting Insert File Path (which requires the BufferTabs plugin), and then picking out the dir right before the .htaccess. If multiple dirs in the dir path have the same name (e.g. a/b/a/), add a distinguishing prefix to the inner dirs (this is rare).
web/VegBIEN/: Moved to datasources/
web/**/.htaccess: Removed "handle DirectoryIndex" rule, which does not appear to be needed with the new dotpath format
web/**/.htaccess: Added "don't rewrite existing paths" and "handle DirectoryIndex" rules to all .htaccess files, not just those for dirs that contain subdirs, to facilitate linking directly to files in the filesystem without first needing to retrofit the applicable .htaccess file.
Renamed www/ back to web/
web/: Moved auxiliary files into the main/ subdir in preparation for having just the web/ dir. Renamed web/ to www/ so it can be replaced with web/main/.
web/main/**/.htaccess: internal redirects using relative paths with .. : Use absolute paths instead so that when the directory is reached through a symlink, the redirect will still work. Note that relative paths without .. do not need to be absolute paths because the subtree structure is the same (just the parent dirs are different).
Added web/main/Redmine/svn-web/
