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When I use Writekey.vi to modify a config file, and then use close configdata.vi to save the file.
Why every key will add a spce before and after "=".
Just try open block diagram of 'Write Key.vi' and then open its sub-VI 'Add Key.vi'. You'll find that, adding space between is intended in this sub-VI, as shown below.
When you open the config file the whole file is read into memory. When writing the file the whole file is written, so all keys (modified or not) will be "rewritten".
The space before and after the = as well as the empty line between sections have been introduced for better readability as far as I know.
The file will still be read correctly by older versions of the config file VIs in case you're concerned about that.