IMPORTANT: re-preparation can only be done with --prepare-redo

Until now, the preparation phase was always executed before the final build
phase when running `./project make'. But when it becomes necessary, project
preparation can be slow and will un-necessarily slow down the project while
the project is growing (focus is on the analysis that is done after
preparation).

With this commit, preparation will be done automatically the first time
that the project is run (`.build/software/preparation-done.mk' doesn't
exist). However, after preperation is complete once, future runs of
`./project make' won't do preparation any more (by calling
`top-prepare.mk'). They will directly call `top-make.mk' for the analysis.

To manually invoke preparation after the first attempt, the `./project
make' script should be run with the new `--prepare-redo' option.

Also, since the preparation phase is now automatically done before the
analysis phase, the long notice that describes running `./project make' at
the end of the preparation phase has been removed in `top-prepare.mk'. It
now just prints a short line, saying the preparation has been complete.

Finally, when the project has not been run with the proper group
configuration, it ends with an `exit 1' so the main `./project' script
doesn't proceed any further.

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