Manually installed core packages no longer show up

[winstliu]

Prerequisites

• Put an X between the brackets on this line if you have done all of the following:
  • Reproduced the problem in Safe Mode: http://flight-manual.atom.io/hacking-atom/sections/debugging/#using-safe-mode
  • Followed all applicable steps in the debugging guide: http://flight-manual.atom.io/hacking-atom/sections/debugging/
  • Checked the FAQs on the message board for common solutions: https://discuss.atom.io/c/faq
  • Checked that your issue isn't already filed: https://github.com/issues?utf8=✓&q=is%3Aissue+user%3Aatom
  • Checked that there is not already an Atom package that provides the described functionality: https://atom.io/packages

Description

With the new Notification format, core packages that were manually installed no longer show up in the "Non-Core Packages" section. This was useful for cases when the manually installed version was the culprit, and now we have no way of figuring that out.

Steps to Reproduce

1. Link a core package
2. Trigger an error somehow (done easily through init.coffee)
3. Copy the notification contents and paste them somewhere

Expected behavior: Non-Core Packages to include the manually installed package

Actual behavior: Manually installed package is not listed

Reproduces how often: 100%

Versions

Atom    : 1.15.0-dev-4eb3f22
Electron: 1.4.15
Chrome  : 53.0.2785.143
Node    : 6.5.0

apm  1.15.3
npm  3.10.5
node 4.4.5 x64
python 2.7.12
git 2.10.0.windows.1
visual studio 2015

/cc @damieng