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Richard, can you think of a good way to make this configurable? I agree that this would be great but I fear it would get messy quickly because there are so many possible combinations of how to select a "good" candidate. I guess also it depends on what you mean by "configurable" -- I tend to read it as "flick a switch in the config file" while so often in DSpace it means "you can write a custom Java class that implements your custom logic".
For your specific case, the HTML trees -- is the index.html really not what you want to index, if the choice is index that one or index no file at all for the item? I guess at the end of the day it really depends on the content in your repository, but 'my' repository managers all thought that indexing _something_ is better than indexing nothing. The good old false positives vs false negatives trade-off I suppose...