util: explicitly close all AutoFiles that have been written

fclose(3) may fail to flush the previously written data to disk, thus a failing fclose(3) is as serious as a failing fwrite(3).

Previously the code ignored fclose(3) failures. This PR improves that by changing all users of AutoFile that use it to write data to explicitly close the file and handle a possible error.

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Other alternatives are:

1. fflush(3) after each write to the file (and throw if it fails from the AutoFile::write() method) and hope that fclose(3) will then always succeed. Assert that it succeeds from the destructor :roll_eyes:. Will hurt performance.
2. Throw nevertheless from the destructor. Exception within the exception in C++ I think results in terminating the program without a useful message.
3. (this is implemented in the latest incarnation of this PR) Redesign AutoFile so that its destructor cannot fail. Adjust all its users 😭. For example, if the file has been written to, then require the callers to explicitly call the AutoFile::fclose() method before the object goes out of scope. In the destructor, as a sanity check, assume/assert that this is indeed the case. Defeats the purpose of a RAII wrapper for FILE* which automatically closes the file when it goes out of scope and there are a lot of users of AutoFile.