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Many of the files appear to contain JavaScript functions in a format generated by Adobe Dreamweaver, making it almost certain that at least some of the websites were developed in that editor. This was first pointed out by Reddit user sq00q. Also note that the username spells "boobs" upside down in leet.
For example, starwarsweb.net contains the four following functions, first commented out which is funny and has some version comments:
function MM_swapImgRestore() { //v3.0
function MM_preloadImages() { //v3.0
function MM_findObj(n, d) { //v4.01
function MM_swapImage() { //v3.0
and then repeated on a body onload. Here MM_ stands for MacroMedia, and is mentioned e.g. at:
Doing:
git grep MM_swapImage | sed -r 's/\/.*//' | sort -u | wc
on github.com/cirosantilli/cia-2010-websites-dump currently gives 64 hits out of 421 websites.
The same signatures are also found on the early websites from 2004 such as alljohnny.com.
The approximate version history is:

Ancestors (15)

  1. HTML analysis
  2. Fingerprints
  3. Methodology
  4. CIA 2010 covert communication websites
  5. Central Intelligence Agency
  6. American intelligence agency
  7. United States Intelligence Community
  8. Intelligence community
  9. Secret service
  10. Espionage
  11. War
  12. Social science
  13. Scientific method
  14. Science
  15. Home