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I noticed the issue when I first went to run

defaults write com.apple.finder AppleShowAllFiles YES

in OS X Terminal (10.11.2) but this was returned

bash: /usr/bin/defaults: Invalid argument

I'm not sure what is going on with defaults, but I also have a similar issue with brew:

/bin/bash: /usr/bin/dirname: Invalid argument

I clearly broke something (or perhaps malware), but not sure how I did it or when it happened. This is causing all sorts of issues. Any thoughts on fixing it?

My PATH variable looks like this:

/Users/username/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin:/usr/local/MacGPG2/bin:/usr/texbin:/Users/username/.rvm/bin

EDIT: I noticed my issue is similar to this one: OS X Yosemite Hard Disk Errors even after Repairing them but there's no resolution.

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    Please add your PATH (echo $PATH) and check your history file and env – klanomath Jan 28 '16 at 23:18
  • $PATH included above. – slightlylost Jan 29 '16 at 20:52
  • What is your prompt? also try with a minimal path - i.e. remove PATH from your .bas* files – Mark Jan 29 '16 at 23:05
  • How do I go about removing PATH from my .bas* files? – slightlylost Feb 26 '16 at 6:19
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Found a solution! I reinstalled El Capitan from the recovery partition (hold command-R while restarting). The errors are now gone.

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