This is actually simpler than it sounds.
If we simplify a couple of statements found in this post to their core meanings (as relating to the term 'cloud') we see that the second paragraph states "When GitHub first launched … clouds were just things in the sky …", then the fourth paragraph compares that past to today with "Now … clouds are mostly computers …".
Basically the first mention of clouds is referring to the fact that ten years ago, everyday conversations in which people used the term "cloud" were almost exclusively about the meteorological phenomenon in which condensed droplets or frozen crystals (usually of water) are suspended in the atmosphere. The second mention of clouds is a statement that in more recent times an everyday conversation including the term "cloud" is more likely to be about 'cloud computing', 'cloud storage', or another similarly computer oriented use of the word "cloud" than about the aforementioned meteorological phenomenon.
Note: The term "cloud" being used in computing is in fact more than ten years old, however the computer related usage didn't really become house-hold vernacular until around 2009-2012*.
*If curious about why I say it became more common around 2009-2012, please notice the increase in search frequency for the term 'cloud computing' from late 2008 to early 2011, and the subsequent increase in search frequency of 'cloud storage' from early 2011 to late 2013 in these graphs: US, World, and note that the drop in 'cloud computing' searches does not slow the similar increase in search frequency of 'cloud' which appears in these graphs: US, World. My guess as to why 'cloud computing' searches slowed then is that more people understood what 'cloud computing' meant, and thus didn't need to search for explanations about it, and/or people no longer felt it necessary to specify that they didn't mean water vapor.)