I edited package.el as per the diff of that commit and eval'd the changed
function.

I can still recreate the problem. Here's what I did:
1. Uninstall git-timemachine using package manager.
2. See that the custom.el is updated (git-timemachine getting removed from
package-selected-packages)
3. Re-install git-timemachine
4. Now the package-selected-packages var gets updated but does not get
written to custom.el automatically.

I believe this issue has been here for a while but I didn't get to chasing
it; doesn't have to do with async install feature revert. It's just that
now it matters more since we have the package-autoremove function.

On Thu, May 21, 2015 at 12:11 PM Artur Malabarba <bruce.connor.am@gmail.com>
wrote:

> Then it sounds like we have a bug. I think I introduced it when
> reverting the async stuff.
> I just pushed a fix, could you try again with the latest master?
>
> 2015-05-21 16:06 GMT+01:00 Kaushal <kaushal.modi@gmail.com>:
> > About 2) the use-package forms happen after I load custom-file.
> >
> > I just manually deleted those 3 packages and reinstalled them from the
> > package manager and then M-x package-autoremove displayed "Nothing to
> > autoremove". But I noticed that that process did not update the
> > package-selected-packages to the custom.el. I had to manually eval
> >
> > (package--save-selected-packages (package--find-non-dependencies))
> >
> > in order to update the custom.el
> >
> > Before that, of course, after each emacs restart, package.el was trying
> to
> > autoremove those 3 packages.
> >
> > On Thu, May 21, 2015 at 10:58 AM Artur Malabarba <
> bruce.connor.am@gmail.com>
> > wrote:
> >>
> >> 2015-05-21 15:35 GMT+01:00 Kaushal <kaushal.modi@gmail.com>:
> >> > I just updated to the latest commit on emacs master and tried out
> >> > package-autoremove.
> >> >
> >> > That suggested removing 3 packages (symon, minibuffer-line,
> >> > git-timemachine), out of which I actually use 2: minibuffer-line,
> >> > git-timemachine.
> >> >
> >> > For example, I have this in my init:
> >> >
> >> > ;; Display date+time in the minibuffer instead of in the mode-line
> >> > (use-package minibuffer-line
> >>
> >> There are two possibilities for why this happened.
> >>
> >> 1. The first time you start Emacs after the commit that introduced
> >> selected-packages, package.el will try to guess which of your packages
> >> were explicitly installed by you, and which were pulled in as deps.
> >> It's impossible to know for sure, so this guessing is bound to go
> >> wrong on some instances.
> >>
> >> 2. The list of selected packages is stored with your
> >> custom-set-variables. So, if your `use-package' form comes before your
> >> `custom-set-variables', then that might cause it to not get stored
> >> correctly.
> >>
> >> I'm not sure if there's a global fix we can do for case 2. Either way,
> >> you (the user) can manually fix that by simply trying to install the
> >> package you already have (`minibuffer-line', in this case). You can do
> >> that from the package menu or with `M-x package-install'. You'll get a
> >> message that "package already installed", and then package.el will
> >> store this package in your list of `selected-packages'.
> >> Another way to fix that is to `M-x customize-variable RET
> >> package-selected-packages' and manually add `minibuffer-line' to it.
>