I thought I had solved the vexed problem of using taxonomy for a hierarchical site with nice breadcrumbs, nav menus etc., using a combination of taxonomy_context, pathauto and manually built menus pointing to taxo terms, but apparently Drupal will have the last laugh.
To get the breadcrumbs right, I used a parent term for each vocabulary and aliased this term to a page that is a kind of index page for that section. But, to get the nodes for all child terms on this page, I built the urls manually. For example, if a news section has the parent term 'News' (tid10) and child terms 'Announcements' (tid11) and 'Press Releases' (tid12), I put the following in the url alias:
system path: taxonomy/term/10/11+12
alias : news
The problem
1.) When I tag a story with the parent term of a vocabulary (for example, news) that has been aliased and has manually built urls (taxonomy/term/10/11+12), the category links in the teaser sections and the term names in the breadcrumbs display the original term id (taxonomy/term/10) and not the alias name.
2.) If I run a bulk update using pathauto, I get an extra alias called 'news-0', pointing to the parent terms (taxonomy/term/10), but this is obviously not the solution
3.) I can't avoid manually building the sub-terms into the system path because Drupal does not automatically list on the parent term page the nodes tagged with the child terms of a vocabulary.