re = /\bFOO\b(?![^[\]]*(?:\[\[[^[\]]*]][^[\]\n]*)*]])/m
str = 'Should match the following
lorem ipsum FOO dolor
lorem ipsum FOO dolor [[amet]]
[[lorem]] ipsum FOO dolor [[sit]] amet
Should NOT match the following
lorem ipsum [[FOO]] dolor
lorem [[ipsum FOO dolor]] sit amet
lorem [[ipsumFOOsolor]] sit amet
[[lorem]]
[[ipsum-FOO&dolor-sit.pdf#page=130]]
lorem ipsumFOOsolor sit amet
FOO should be matched below but is not because the double-brackets are not balanced.
lorem FOO [[ipsumFOOsolor]] sit ]] amet'
subst = 'BAZ'
result = str.gsub(re, subst)
# Print the result of the substitution
puts result
Please keep in mind that these code samples are automatically generated and are not guaranteed to work. If you find any syntax errors, feel free to submit a bug report. For a full regex reference for Ruby, please visit: http://ruby-doc.org/core-2.2.0/Regexp.html