The allegations against Appelbaum led to his leaving the project in June. He denied the allegations at the time but has not made any public statements since.
In a statement issued on Wednesday, Tor Project executive director Shari Steele said the investigation had been carried out by a professional and was now complete.
"Many people inside and outside the Tor Project have reported incidents of being humiliated, intimidated, bullied and frightened by Jacob, and several experienced unwanted sexually aggressive behavior from him," Steele said.
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Appelbaum had the highest profile among members of Tor. However when the complaints against him began to mount, organisations of which he was a member were quick to act.
The Debian GNU/Linux project announced that he would not be welcome at its events and revoked his status as a developer. Hacker groups Cult of the Dead Cow and Noisebridge asked him to quit, and the Chaos Computer Club said he would not be allowed to attend any events it organised.
Steele said both the Tor Project and the Tor community would be taking steps to strengthen their ability to handle problems of unprofessional behavior.
"Specifically, the Tor Project has created an anti-harassment policy, a conflicts of interest policy, procedures for submitting complaints, and an internal complaint review process. They were recently approved by Tor’s board of directors, and they will be rolled out internally this week," she said.
"In addition, the Tor community has created a community council to help to resolve intra- community difficulties, and it is developing membership guidelines, a code of conduct, and a social contract that affirms our shared values and the behaviors we want to model. We expect these to be finalised and approved by the community at or before our next developer meeting at the end of September."