This answer to another question states:
Do not forget to clear the connectionStrings first:
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In .Net config files are inherited, so your applications config will inherit settings from your machines config.
The <clear/>
tag will remove any inherited connection strings and thereby avoids confusion and potential problems.
In ASP.Net you may have several inherited connection strings, so this is very common there.
The element removes all sections and section groups from your application that were defined earlier in the current configuration file or at a higher level in the configuration file hierarchy.
http://msdn.microsoft.com/en-us/library/aa903345(v=vs.71).aspx
so for example, if this was a child config file and the parent config file had some settings... you may not want them being inherited so you specify the clear flag to clear it and then use your settings.