one area where SharePoint is not living up to its expectations is document taxonomy. more complicated tree like structures cannot easily be accommodated in SharePoint. although Content Types are great and metadata can be applied as desired, there is no easy way to manage content in multi-level hierarchical structures.
one possible solution is provided by a third party product, Taxonomy Extension:
http://www.sharepartxxl.com/products/taxonomy/default.aspx. this solution allows you to set up a tree structure for tagging and easily apply these tags as metadata to documents. it will also create a category navigation site that allows you to browse links to all tagged documents based on the tree structure. this makes it really easy to navigate your way through the tree even though the actual documents are stored in libraries that do not necessarily match the tree structure.
one problem (as with all custom field types): the tagging doesn't work from within Office applications... maybe a custom document information panel is the solution here?
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