Error “syntax error near unexpected token ‘(‘” in Bash script when selecting files

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I guess your problem is due to the shell extended glob option not set when run from the script. When you claim it works in the command line, you have somehow set the extglob flag which allow to !() globs.

Since the Bash script, whenever started with a #!/bin/bash, starts a new sub-shell, the extended options set in the parent shell may not be reflected in the new shell. To make it take effect, set it in the script after the shebang:

#!/bin/bash

shopt -s extglob

## Going to directory-moving stuff
rm -rf !(composer.json|.git)

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