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add: do not delete stage files before add (#6239)
* add: do not delete stage files before add Because of the way we collect stages and cache them, we were not able to collect them for the `add` without removing them from the workspace. As doing so, we'd have two same/similar stages - one collected from the workspace and the other just created from the `dvc add` in-memory. This would raise errors during graph checks, so we started to delete them and reset them (which is very recently, see #2886 and #3349). By deleting the file before we even do any checks, we are making DVC fragile, and results in data loss for the users with even simple mistakes. This should make it more reliable and robust. And, recently, we have started to keep state of a lot of things, that by resetting them on each stage, we waste a lot of performance, especially on gitignores. We cache the dulwich's IgnoreManager, which when resetted too many times, will waste a lot of our time just collecting them again next time (see #6227). It's hard to say how much this improves, as this very much depends on no. of gitignores in the repo (which can be assumed to be quite in number for a dvc repo) and the amount of files that we are adding (eg: `-R` adding a large directory). On a directory with 10,000 files (in a datadet-registry repo), creating stages on `dvc add -R` went from 64 files/sec to 1.1k files/sec. * add tests * make the test more specific
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