The issue of linking inside and outside the site is something that really needs to be dealt with. Right now, there's a proliferation of different types of link, specified by the @type attribute on the <ref> element; this is the range of instances currently in the XML files (some obviously typos, and some errors):

internal
bibl
detail
external
'detail
pers
name
CORN1
library
special
topics
detal
SIRT1
URI

I propose the following:

1. The @type attribute should just be dropped, and deleted from existing <ref> elements.
2. There should be two types of reference, distinguished by what their @target attribute looks like:
   • <ref target="mol:ADAM4">
   • <ref target="http://some.url/">
   The system should be able to distinguish between them by itself.
3. When the output (XSLT) system sees @target starting with mol:, it knows it has an internal reference. In that case, it constructs a simple link consisting of the relevant @xml:id (which is substring-after(@ref, 'mol:')) followed by .htm.
4. The controller.xql and index.xql files are able to figure out where the relevant @xml:id is, and process it accordingly. So, for instance, if it finds a TEI file in /db/data/ which has that @xml:id attribute on its root element, it processes that; if it finds a person element in PERS1.xml which has that @xml:id, it processes accordingly.
5. When the output (XSLT) system sees @target which does not start with mol:, it assumes an external link, and creates an anchor accordingly.
6. In the case of name tags, which also give rise to links to people, I have already converted all @key="ADAM4" instances to @ref="mol:ADAM4", and links are being created accordingly.

This means that all pages are being served out of the root of the site, and as long as all @xml:ids are unique, everything is accessible in that way. There may still be a couple of details to work out relating to @type on <name> (which is possibly worth keeping, although I don't think it's being used for anything useful at the moment), and the various uses of <bibl> (which I think in some cases ought to be <ref>s).