Issue 1:
Running Atom Version 0.176.0 (0.176.0) and atom-fixmyjs 1.3.0

Originally from sindresorhus/atom-fixmyjs/issues/7

Reproduceable. This appears to be an atom bug, rather than in the atom-fixmyjs package. It looks like there is an npm install error where the fixmyjs dependency doesn't get installed. Previous versions of Atom worked fine, and there were no relevant changes in atom-fixmyjs.

If I go to ~/.atom/packages/fixmyjs and run npm install it works, but with a clean install without manually installing the dependency, if I go to the command palette I can execute FixMyJS the web developer view will show this:

Failed to activate package named 'fixmyjs' Error: Cannot find module 'fixmyjs'
at Module._resolveFilename (module.js:344:15)
at Function.Module._resolveFilename (/Applications/Atom.app/Contents/Resources/app/src/module-cache.js:383:52)
at Function.Module._load (module.js:286:25)
at Module.require (module.js:373:17)
at require (module.js:392:17)
at Object.<anonymous> (/Users/gears/.atom/packages/fixmyjs/index.js:2:15)
at Module._compile (module.js:468:26)
at Object.Module._extensions..js (module.js:486:10)
at Module.load (/Applications/Atom.app/Contents/Resources/app/node_modules/coffee-script/lib/coffee-script/register.js:45:36)
at Function.Module._load (module.js:318:12)
at Module.require (module.js:373:17)
at require (module.js:392:17)
at Package.module.exports.Package.requireMainModule (/Applications/Atom.app/Contents/Resources/app/src/package.js:623:34)
at Package.module.exports.Package.activateConfig (/Applications/Atom.app/Contents/Resources/app/src/package.js:250:12)
at Package.module.exports.Package.activateNow (/Applications/Atom.app/Contents/Resources/app/src/package.js:232:14)
at /Applications/Atom.app/Contents/Resources/app/src/package.js:682:29
at Emitter.module.exports.Emitter.emit (/Applications/Atom.app/Contents/Resources/app/node_modules/event-kit/lib/emitter.js:82:11)
at CommandRegistry.module.exports.CommandRegistry.handleCommandEvent (/Applications/Atom.app/Contents/Resources/app/src/command-registry.js:224:20)
at /Applications/Atom.app/Contents/Resources/app/src/command-registry.js:3:61
at CommandPaletteView.module.exports.CommandPaletteView.confirmed (/Applications/Atom.app/Contents/Resources/app/node_modules/command-palette/lib/command-palette-view.js:120:32)
at CommandPaletteView.module.exports.SelectListView.confirmSelection (/Applications/Atom.app/Contents/Resources/app/node_modules/go-to-line/node_modules/atom-space-pen-views/lib/select-list-view.js:336:21)
at space-pen-li.<anonymous> (/Applications/Atom.app/Contents/Resources/app/node_modules/go-to-line/node_modules/atom-space-pen-views/lib/select-list-view.js:140:19)
at HTMLOListElement.jQuery.event.dispatch (/Applications/Atom.app/Contents/Resources/app/node_modules/archive-view/node_modules/atom-space-pen-views/node_modules/space-pen/vendor/jquery.js:4676:9)
at HTMLOListElement.elemData.handle (/Applications/Atom.app/Contents/Resources/app/node_modules/archive-view/node_modules/atom-space-pen-views/node_modules/space-pen/vendor/jquery.js:4360:46)

Issue 2:
I made a package called tidy-markdown, that depends on an npm package of the same name (and currently the same version too). The atom package is just a thin wrapper around the npm package, so it didn't seem like it should have a different name, and I certainly didn't want to add a "atom-" prefix to the actual package name.

However, when I run apm install tidy-markdown, the resulting installation is missing the tidy-markdown dep (~/.atom/packages/tidy-markdown/node_modules/tidy-markdown). The other dep, emissary, installs just fine. The installation doesn't produce any error or warning, it just fails when I open atom, resulting in this error: notslang/atom-tidy-markdown#1

Also, if I cd into the directory of the package (~/.atom/packages/tidy-markdown) and just run apm install, the tidy-markdown npm package is installed into ~/.atom/packages/tidy-markdown/node_modules/tidy-markdown, and works as expected.