Improve doxygen files clean-up

Task to improve changes from PR #387

Below are suggestions from @awulkiew which I intend to work on:

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Instead of clearing out the index dir in the `index/make_qbk.py` and doing the same in the `make_qbk.py`, `index/make_qbk.py` could be executed with `--release-build` option and cleanup related to the index could be done only there.

There are generated `*.qbk` files in directories doc/generated and doc/index/generated which are not needed. Also `doc/html/geometry_HTML.manifest` file. Ideally they probably should be removed as well, but this should be done after `b2` is called. But since `b2` can run `make_qbk.py` and the script is then executed before quickbook it is impossible to implement the cleanup of generated qbk files in this single script. Maybe it could be done in a separate cleanup script run by b2 after building docs from qbk files, but I don't know how exactly.

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