Issue 1:
[Enter steps to reproduce below:]

Delete a file that is already in project

Open that session.

Atom Version: 1.0.1-375cf27

System: "Sabayon Linux

Thrown From: Atom Core

Stack Trace

Uncaught Error: ENOENT: no such file or directory, open '/home/v3ss/workspace/phwa.re/gui/phwabe/source/class/phwabe/utils/list/InfiniListDebounce.js'

At events.js:141

Error: ENOENT: no such file or directory, open '/home/v3ss/workspace/phwa.re/gui/phwabe/source/class/phwabe/utils/list/InfiniListDebounce.js'
at Error (native)
at EventEmitter.ipc.sendSync (/opt/atom/resources/atom.asar/renderer/api/lib/ipc.js:21:31)
at Object.exports.require (/opt/atom/resources/atom.asar/renderer/api/lib/remote.js:160:16)
at Object.<anonymous> (/home/v3ss/.atom/init.coffee:1:19)
at Object.<anonymous> (/home/v3ss/.atom/init.coffee:1:1)
at Module._compile (module.js:452:26)
at Object.requireCoffeeScript (/opt/atom/resources/app.asar/node_modules/coffee-cash/lib/coffee-cash.js:85:19)
at Module.load (module.js:347:32)
at Function.Module._load (module.js:302:12)
at Module.require (module.js:357:17)
at require (module.js:376:17)
at Atom.module.exports.Atom.requireUserInitScript (/opt/atom/resources/app.asar/src/atom.js:924:20)
at Atom.module.exports.Atom.startEditorWindow (/opt/atom/resources/app.asar/src/atom.js:644:14)
at Object.<anonymous> (/opt/atom/resources/app.asar/src/window-bootstrap.js:12:8)
at Object.<anonymous> (/opt/atom/resources/app.asar/src/window-bootstrap.js:23:4)
at Module._compile (module.js:452:26)
at Object.loadFile [as .js] (/opt/atom/resources/app.asar/src/babel.js:162:21)
at Module.load (module.js:347:32)
at Function.Module._load (module.js:302:12)
at Module.require (module.js:357:17)
at require (module.js:376:17)
at setupWindow (file:///opt/atom/resources/app.asar/static/index.js:96:23)
at window.onload (file:///opt/atom/resources/app.asar/static/index.js:36:7)

Commands

Config

{
"core": {
"disabledPackages": [
"language-ruby-on-rails",
"mobile-preview",
"atom-html-preview",
"color-picker",
"run-command",
"runcoderun",
"whitespace",
"svg-preview",
"autosave",
"autocomplete-jedi",
"autocomplete-plus-async",
"cute-cursor",
"pulsing-cursor",
"neon-selection",
"atom-lint",
"animation-showcase",
"tree-view-open-files",
"autocomplete",
"ease-blink",
"highlight-line",
"minimap-highlight-selected",
"minimap",
"markdown-writer",
"atom-alignment",
"autocomplete-atom-api",
"fancy-input",
"sublime-tabs",
"spell-check",
"tool-bar-main",
"tool-bar",
"flex-tool-bar",
"atom-ternjs",
"gutter-shadow",
"local-history",
"tab-rename",
"open-in",
"pigments",
"linter",
"goto",
"cursor-blink-interval"
],
"ignoredNames": [
"*.pyc",
"/home/v3ss/workspace/phwa.be/condaenv",
"/home/v3ss/workspace/phwa.be/pypyenv",
"*.zip",
"*.tar",
".hg"
],
"autoHideMenuBar": true,
"themes": [
"steam-pirate-ui",
"steam-pirate-syntax"
]
},
"editor": {
"preferredLineLength": 120,
"tabLength": 4,
"confirmCheckoutHeadRevision": false,
"autoIndentOnPaste": false,
"scrollSensitivity": 120,
"invisibles": {},
"showIndentGuide": true,
"lineHeight": 1.35,
"scrollPastEnd": true,
"zoomFontWhenCtrlScrolling": false,
"fontSize": 12,
"fontFamily": "NK57 Monospace"
}
}

Installed Packages

# User
auto-reveal-in-sidebar, v0.5.0
autocomplete-plus-python-jedi, v0.3.6
autohide-tree-view, v0.20.2
block-cursor, v0.13.1
block-travel, v1.0.2
build, v0.38.0
editorconfig, v1.0.0
file-icons, v1.5.8
file-type-icons, v0.7.0
hashrocket, v0.4.8
highlight-column, v0.5.0
highlight-selected, v0.10.1
language-javascript-better, v1.5.0
language-nim, v0.2.2
linter-coffeelint, v0.3.2
linter-csslint, v0.0.14
linter-flake8, v1.4.2
linter-jshint, v0.1.7
linter-tidy, v1.0.1
linter-xmllint, v0.0.6
minimap-bookmarks, v0.1.0
minimap-find-and-replace, v4.2.0
minimap-selection, v4.2.0
pdf-view, v0.22.0
script-runner, v1.8.3
steam-pirate-syntax, v0.3.0
steam-pirate-ui, v0.6.1
symbols-tree-view, v0.9.3
tabs-to-spaces, v0.11.0
web-browser, v1.5.0

# 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.