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Adjust tools READMEs for new markdown docs

Stephan Lachnit requested to merge slachnit/allpix-squared:p/mddocs-tools-readme into staging_docs

Note on the Octree section: I'm not entirely certain why it is there, the section looks kinda odd in the manual (link). Since it is properly referenced and the embedded code is properly annotated, I don't think this is necessary, hence I removed it.

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