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I... delete everything else (including db/ and dse/ directories).
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It is usually OK to delete the db directory. A couple of situations where you should not delete it:
(1) You are using smart compilation mode and want Quartus to skip a step (usually Analysis & Synthesis) when it is not needed.
(2) You are using incremental compilation. The top-down flow stores the incremental compilation files in the db directory. The bottom-up flow stores files there after you import from a .qxp file.
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.qsf is the main Quartus project file of nearly trivial contents...
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I think you mean the .qpf file. It lists the names of the revisions. Each revision name in the .qpf file matches the name of a .qsf file. Revisions let you have multiple .qsf files (and the associated report files after you compile with them) with different combinations of settings. You can work with revisions using "Project --> Revisions".
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I must admit I don't know exactly what .qdf is used for or if it's essential.
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A .qdf file is a Quartus defaults file. See the header comments in your .qsf file for some information about .qdf files. A .qdf file has the default values of all settings that are not stated explicitly in the .qsf file. If you don't have a .qdf file in your Quartus project directory, Quartus uses the .qdf file included in the Quartus installation.
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