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docs: update stale links (#13776)

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Co-authored-by: Sediman <jason@sediman.com>
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plugins/bedtools/README.md
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# Bedtools plugin
This plugin adds support for the [bedtools suite](http://bedtools.readthedocs.org/en/latest/):
This plugin adds support for the [bedtools suite](https://bedtools.readthedocs.io/en/latest/):
* Adds autocomplete options for all bedtools sub commands.