For anyone else who arrives here while searching for an automatic fill action or button: there is no such thing, but you can easily use a combination of ManicTime's other features instead.

There are two basic mechanisms for automatically filling any gaps if you make use of Autotags:
- The "Auto fill gaps smaller than X seconds" setting found in the Autotag editor (this will fill half of the gap with the previous tag and the other half with the following tag). If the gap is larger then the gap remains empty.
- If you want to blanket fill any gaps no matter the duration then you can also use the "Copy tags to autotags" option in the Autotag editor and add an "Absorb" autotag based on the "Computer Activity" timeline (this will always take the previous tag, no dividing). To do so, right click the "Computer Activity" timeline, select Add to Autotag, give this autotag a unique name. Open the Autotag editor, select the new autotag and edit it. On the Advanced tab you can pick "Absorb".

Once the autotag timeline is completely filled you can use it as a source for your timesheet reports instead of the Tags timeline.

However, I was a bit reluctant to use the above in my autotags timeline because the documentation does mention that these fill methods are just a best guess (especially true for the Absorb autotag). The trick then is that you can stay away from modifying the defualt Autotags timeline, open the Timeline editor and add a second Autotags timeline with a different name. This second Autotags timeline will have its own settings and its own set of rules, at which point you can configure it however you want. But it will also change the behavior of the "Copy Autotags to Tags" button: instead of directly copying things there will be a menu to pick which autotags timeline to copy from.

This way one can copy from the regular Autotags timeline to Tags first, then maybe manually tag some of the gaps, and finally run the copy action but from the second autotags timeline.

Someone from support showed me that this is actually already possible. Just change your autotag settings (even if you aren't really using autotags) to autofill gaps smaller than a specified amount of time.

I completely agree, and I think this is a really important one. Even if we tag/autotag everything perfectly, there will be slivers of time when moving between applications (on the desktop for example, or a quick check of email) and it's very common that I'd just want to lump all that together, especially if I was working on the same project before and after checking my email, for example. I agree with the posters suggestion of a threshold of time or something, like if it's less thatn five minutes, just bring the tags together.