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Flush file before passing it to next function

Nico requested to merge (removed):flush-file-before-pass into master

When downloading a repo index, the downloaded index got written to a file with .write() in a with clause. Before the file got actually written to the disk, it got already passed into the next function, resulting in a VerificationException:

JAR signature failed to verify: /tmp/tmppq2r51r0
jarsigner: java.util.zip.ZipException: zip file is empty

This behavior got introduced in 869cc114.

I've found this bug with help of Repomaker's tests: repomaker!215 (comment 148994053)

CC @grote

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