If that doesn't work for you, this might:
history 1 | awk '{print $2}' | awk 'BEGIN {FS="|"}{print $1}' | sort | uniq -c | sort -n | tail | sort -nr
What that doesn't give you is the command tree, for example "git commit" vs "git checkout". It just does "git".
[edit, added gem link] The gem is here https://github.com/paulmars/huffshell
import sys
import collections
tree = lambda: collections.defaultdict(lambda: [0, tree()])
def printtree(node, indent=0):
padding = indent * ' '
for word, (count, child) in node.iteritems():
print "%s%s %d" % (padding, word, count)
printtree(child, indent + 2)
wordtree = tree()
for line in sys.stdin:
node = wordtree
for word in line.split():
node[word][0] += 1
node = node[word][1]
printtree(wordtree)