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use markdown for the documentation (#1474)
* add doc.md * use h2 for doc sections * use h3 for doc commands/options/vars * use backticks instead of quotes in the doc * merge multiple commands/options in the doc * change header levels in the doc * add man page sections to the doc * remove extra spaces in headers in the doc * add man and plain conversions of the doc * update doc * add missing flags to the doc * replace the old documentation with the new one * remove old doc files * remove the doc instructions from CONTRIBUTING.md * change the links to the doc * shorten long links in the readme
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