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.
>