Stuck on a bug or two, I instead built a new Preferences page:

The main reason I wanted that was to allow enabling debug logging at runtime. But I've also wanted to expose annex.diskreserve and annex.numcopies settings to the webapp user. Might as well let them control whether it auto-starts too.

Had some difficulty deciding where to put this. It could be considered additional configuration for the local repository, and so go in the local repository edit form. However, this stuff can only be configured for local repositories, and not remotes, and that same form is used to edit remotes, which would lead to inconsistent UI and complicate the code. Also, it might grow to include things not tied to any repository, like choice of key/value backends. So, I put the preferences on their own page.

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Also, based on some useful feedback from testing the assistant with a large number of files, I made the assistant disable git-gc auto packing in repositories it sets up. (Like fsck, git-gc always seems to run exactly when you are in a hurry.) Instead, it'll pack at most once a day, and with a rather higher threshold for the number of loose objects.