Issue 1:
When changing branches in git while one of the files that are being rewritten (due to the branch switch) is open in atom this happens:

Atom Version: 0.199.0

System: linux 3.14.39-1-lts

Thrown From: Atom Core

Stack Trace

Uncaught Error: ENOENT: no such file or directory, open '/home/despairblue/vcs/git/scegratoo3/app/scripts/services/treenodeattribute.js'

At events.js:141

Error: ENOENT: no such file or directory, open '/home/despairblue/vcs/git/scegratoo3/app/scripts/services/treenodeattribute.js'
at Error (native)

Commands

-0:48.2.0 symbols-view:toggle-file-symbols (atom-text-editor.editor.is-focused)
-0:47.5.0 editor:consolidate-selections (atom-text-editor.editor.mini.is-focused)
-0:47.5.0 core:cancel (atom-text-editor.editor.mini.is-focused)
-0:46.1.0 command-palette:toggle (atom-text-editor.editor.is-focused)
-0:43 core:backspace (atom-text-editor.editor.mini.is-focused)
-0:40.9.0 core:confirm (atom-text-editor.editor.mini.is-focused)
-0:40.9.0 git-plus:new-branch (atom-text-editor.editor)
6x -0:36.8.0 core:backspace (atom-text-editor.editor.mini.is-focused)
3x -0:27.5.0 editor:move-to-beginning-of-word (atom-text-editor.editor.mini.is-focused)
-0:25 core:confirm (atom-text-editor.editor.mini.is-focused)

Config

{
"core": {
"excludeVcsIgnoredPaths": false,
"disabledPackages": [
"welcome",
"metrics",
"autocomplete",
"incremental-search",
"Tern",
"grunt-runner",
"tree-view-open-files",
"tree-view-breadcrumb",
"atomatigit",
"themed-settings",
"linter-scspell",
"filetype-color",
"atom-pair",
"linter-eslint",
"es-navigation",
"autocomplete",
"tab-smart-sort",
"starred-package-installer",
"zentabs",
"linter-jshint",
"block-cursor",
"test-status",
"minimap",
"minimap-color-highlight",
"minimap-find-and-replace",
"minimap-git-diff",
"minimap-highlight-selected",
"travis-ci-status",
"pane-layout-plus",
"symbols-tree-view",
"package-cop",
"navigate"
],
"projectHome": "/home/despairblue/vcs/git/",
"destroyEmptyPanes": false,
"themes": [
"one-dark-ui",
"solarized-dark-syntax"
],
"autoHideMenuBar": true
},
"editor": {
"fontFamily": "Source Code Pro, Symbola, Droid Sans Fallback",
"lineHeight": 1.4,
"showIndentGuide": true,
"scrollPastEnd": true,
"invisibles": {},
"fontSize": 13,
"softWrap": true
}
}

Installed Packages

# User
angularjs, v0.1.0
atom-alignment, v0.12.1
atom-color-highlight, v3.0.9
atom-ternjs, v0.5.30
atom-zeal, v0.1.0
autocomplete-emojis, v2.2.2
autocomplete-paths, v1.0.2
block-travel, v1.0.2
bug-report, v0.7.0
color-picker, v1.7.0
compare-files, v0.4.1
docblockr, v0.7.1
editorconfig, v1.0.0
file-icons, v1.5.5
git-log, v0.3.0
git-plus, v4.5.0
go-plus, v3.3.11
grammar-token-limit, v0.1.1
highlight-selected, v0.9.3
indentation-indicator, v0.5.1
javascript-snippets, v1.0.0
keybinding-cheatsheet, v0.0.9
language-dockerfile, v0.1.0
language-dot, v1.6.0
language-fish-shell, v1.0.2
language-haskell, v1.0.0
language-javascript-better, v1.5.0
language-latex, v0.6.1
language-nimrod, v0.1.0
language-puppet, v0.12.0
language-tss, v0.1.0
latex, v0.23.4
linter, v0.12.2
linter-coffeelint, v0.2.3
linter-htmlhint, v0.0.15
linter-js-standard, v0.2.5
linter-js-yaml, v1.0.1
linter-puppet-lint, v0.2.9
linter-shellcheck, v0.0.7
markdown-scroll-sync, v0.3.3
open-last-project, v0.4.1
pdf-view, v0.22.0
project-manager, v1.15.5
regex-railroad-diagram, v0.7.4
tabs-to-spaces, v0.10.0

# Dev
No dev packages

Issue 2:
Some repro steps that I gathered from the existing issues:

Have a file open in branch something that doesn't exist in branch atom

git checkout atom

ENOENT 💥

OR

Have a file open in Atom that will be affected by git rebase

git rebase

ENOENT 👎

OR

Just simply rename a file outside of Atom that's currently open inside of Atom.