Use as follows:

[%- ## Some type of file header ### -%]

See "Chomping Whitespace" in documentation:
  
http://www.template-toolkit.org/docs/manual/Syntax.html#section_Chomping_Whitespace

By the way, this applies not only to comments.

-- 
Sincerely yours,
Oleg Kostyuk (CUB-UANIC)

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