web/BIEN3/Redmine/.htaccess: enable redirects that avoid using a subdir's .htaccess

web/BIEN3/Redmine/.htaccess: point this to the Redmine root instead of to the wiki, to avoid the need to append /main

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: RewriteOptions: Redirect dir paths without the trailing / to the datasource's homepage, and let dir paths with the trailing / point to the directory index. This is the opposite of the way it was before, and is more intuitive because the trailing / indicates a directory listing, while the trailing / would generally be omitted when linking to the datasource itself.

web/**/.htaccess: handle DirectoryIndex subrequests, which append "index" to the dir

web/**/.htaccess: RewriteOptions: Removed inherit because if the destination is not found in the current dir, a 404 should be returned instead of trying to invoke the parent dir's fallback handler (which applies only to paths in the parent dir). Ideally, we would use InheritBefore to get the subdomain preprocessing, etc., but the parent dir's fallback handler would still need to be turned off somehow when the rule was being run by a subdir.

web/**/.htaccess: RewriteOptions: Added AllowNoSlash (available in Apache 2.4) so dir paths without the trailing / can be parsed by mod_rewrite

web/**/.htaccess: parse dotpath in the query string: Use just dotpath instead of dotpath.php because the extension is added automatically by MultiViews

web/**/.htaccess: parse dotpath in the query string: Remove any index.* suffix, which is added by MultiViews in Apache 2.4

web/**/.htaccess: Removed "handle DirectoryIndex" rule, which does not appear to be needed with the new dotpath format

web/**/.htaccess: Restrict redirection only of fully-existing paths, rather than of any path whose subdir exists, in order to avoid having to hardcode the absolute path to the directory containing the .htaccess file. This more restrictive approach still works because if the subdir exists and contains an .htaccess file, this (outer) .htaccess file's RewriteRules will be ignored completely until the inner .htaccess file's rules have been run, so that any subdir redirects will happen first. This "hole-punch" effect causes an existing filesystem path to always take priority over a virtual path (i.e. a redirect) defined in an outer .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: Support dotpaths in the query string instead of in the path, so that non-dotpath paths don't need to be suffixed with / to prevent their filenames from being interpreted as dotpaths. Putting dotpaths in the query string still requires only one character between the host and the path, but it's ? instead of / . ? is in many ways more natural, because the dotpath is a non-filesystem string to be parsed rather than something that's already a filesystem path. This change also avoids the need to strip trailing /s in many RewriteRules, because the dotpath mechanism is no longer appending them.

Added web/main/VegBIEN/Redmine/