[feat]: `zinit update --all` should reflect changes made on the filesystem and plugin list

[seivan]

Feature request

I got a zinit_plugins.zsh file where I load all my plugins, completions and etc.
Occasionally, I add and remove something, but the zinit_downloads doesn't reflect the changes.

For instance adding this to zinit_plugins.zsh

zinit ice lucid blockf wait depth"1" as"completion"
zinit snippet https://github.com/zsh-users/zsh-completions/blob/master/src/_git-flow

If I remove those lines, the relevant files in zinit_downloads subdirectories that are no longer relevant should be gone if I run zinit update --all

Another issue is, if I were to test things out and say delete the file at zinit_downloads/completions/_git-flow manually
doing zinit update --all does not re-add it to zinit_downloads/completions even though it's part of my zinit_plugins.zsh

Either zinit update --all should resolve both of those, or the cleanup portion should be part of something like zinit cleanup --all.