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You may solve this problem adding new framework with desired alias and commands in tool path. For example, with alias lss and tool path ls -la && ls -la .. . And when you invoke lss command in popup, you'll get listed your current directory and it's parent one.

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sounds logical?

but see what you get:

Cannot run program "redocrine2" (in directory "/home/cordoval/sites/Symfony/Memorize-Scripture-2"): java.io.IOException: error=2, No such file or directory

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Did you provide full path to executable in the tool path? Is the command you provided in the tool path executed correctly in system console?

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I did

"$PhpExecutable$" "$ProjectFileDir$/app/console" doctrine:schema:drop --force && "$PhpExecutable$" "$ProjectFileDir$/app/console" doctrine:schema:create && "$PhpExecutable$" "$ProjectFileDir$/app/console" doctrine:data:load

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But there is no redoctrine2 in provided tool path. Maybe this is a problem of doctrine configuration?

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no that is the alias, it could be anything

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Some more questions: what is your PhpStorm version and did you type exactly the alias? (Seems that redocrine2 may be redoctrine2). Was the first string of output something like "C:\opt\php5.3.5\php.exe" "C:\Users\eshaverdova\PhpstormProjects\ToolTestProject/app/console" doctrine:schema:drop --force && "C:\opt\php5.3.5\php.exe" "C:\Users\eshaverdova\PhpstormProjects\ToolTestProject/app/console" doctrine:schema:create && "C:\opt\php5.3.5\php.exe" "C:\Users\eshaverdova\PhpstormProjects\ToolTestProject/app/console" doctrine:data:load or just redocrine2?

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unbutu latest
EPA latest Phpstorm version

did see just redoc or whatever alias is
...

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This is a bug then, and i could not reproduce it. The only idea is that actual input differed from alias.

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I will try using the path rather than $var$ variables    
don't give up, grab an ubuntu machine and try reproducing it     

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ok, i won't give up

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