tool/downloader.rb: Stop caching already existing files

Previously, the script was caching any file already present in the
destination directory, regardless of its origin. This caused issues
when the directory contained files copied from external sources like
`autoreconf --install`.

For example:
1. `./autogen.sh --install` copies `config.guess` and `config.sub`
   from the system to `./tool`.
2. `ruby tool/downloader.rb -d tool -e gnu config.guess config.sub`
   treats those files as if they were downloaded and caches them.
3. Removing the files: `rm tool/config.guess tool/config.sub`.
4. Running the downloader again, it mistakenly restores the cached
   files instead of downloading fresh versions.

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