Quick answer: Jefferson did NOT think the Jane was a pirate ship… but it was a pretty close call in a time when merchant ships could act as privateers, and switch back to being regular trading vessels, and essentially all ships were armed to the teeth.
To find the answer to this question, I started by first looking for the entire collected works of Thomas Jefferson. I figured that the answer would be somewhere in his collected writings, and I had suspicion that I could probably find every instance of the word “Jane” and jump right to the answer.
A query [ Thomas Jefferson collected writings ] led me to a few good collections such as the “Online Library of Liberty” which has the complete writings. (As does www.Constitution.org and the Jefferson collection at Scribd.com.)
The trick with such collections is to very carefully check to make sure it’s the COMPLETE collection (and not just the “Founding Documents” collection, or just his letters, or similar subset). ALSO, be careful that the collection isn’t larded up with lots of notes and commentaries, especially at the beginning of each chapter when a learned scholar writes his analysis of what lies in the chapter to come… these aren’t useful for our primary document research and can seriously mislead you if you're not careful in your search.
My initial strategy was to find a collection, then use site: to search within the collection. But, alas, of the collections I found, all of them have broken up the documents into non-SITE:-searchable groups. The Scribd collection, for instance, has all 12 volumes of his collected words, but each volume is in a different subdirectory, and there isn’t a common root that I could use site: over!
So I kept looking for such a site: searchable collection and after a few clicks found www.history1700s.com/etext/html/texts/jefferson/ as exactly what I was looking for. A quick site: search and… I found 2 hits.
Huh? THAT didn’t make any sense. I know that there must be more hits than that (after all, Jefferson’s mother, sister and baby daughter were all named “Jane”).
So I kept looking for a better resource.
In a separate tab I pursued another strategy—to see if I could find some document written by Jefferson in 1793 about the Jane as a ship. So I used my old friend the AROUND operator like this to find the word "ship" within 3 words of the word "Jane" -- that removed any spurious hits.
This in turn led me to a number of books that collected the writings of Jefferson. The first hit was “A message of the President of the United States to Congress relative to France and Great-Britain: delivered December 5, 1793, with the papers therein referred, to which are added the French originals.” This is a scanned book published in 1793 (so I think it’s a pretty reputable source).
Reading the text (see below) it became clear that Mr. Genet was accusing the Jane of being an English privateer. The Jane has a letter of marquee (which would allow her to attack foreign vessels). And why else would she install 2 new cannons with carriages onboard? Jefferson, though, argues that this is just ordinary precautions that any vessel would take in time of war and strife.
This was all a tricky political question because of the neutrality of the US wrt the war in France.
From the note (in a slightly more readable format):
“Mr Genet in his letter of July 9th requires that the ship Jane which he calls an English privateer shall he immediately ordered to depart and to justify this he appeals to the 23d article of our treaty which provides that it shall not be lawful for any foreign privateer to sit their ships ill our ports to sell what they have taken or purchase victuals &c The ship Jane is an English merchant vessel which has been many years employed in the commerce between Jamaica and these states She brought here a cargo of produce from that island and was to take away a cargo of flour Knowing of the war when he left Jamaica and that our coast was lined with small French privateers she armed for her defence and took one of those commissions usually called Letters of Marque. She arrived here safely without having had any encounter of any sort. Can it be necessary to say that a merchant vessel is not a privateer That though she has arms to defend herself in time of war in the course of her regular commerce this no more makes her a privateer than a husbandman following his plough in time of war with a knife or pistol in his pocket is thereby made a soldier. The occupation of a privateer is to attack and plunder that of a merchant vessel is commerce and self preservation The article excludes the former from our ports and from selling what she has acquired by war to shew it did not mean the merchant vessel and what she had acquired by commerce. Were the merchant vessels coming for our produce forbidden to have any arms for their defence every adventurer who has a boat or money enough to buy one would make her a privateer our coasts would swarm with them foreign vessels must cease to come our commerce must be suppressed our produce remain on our hands or at least that great portion of it which we have not vessels to carry away our ploughs must he laid aside and agriculture suspended. This is a sacrifice no treaty could ever contemplate and which we are not disposed to make out of mere complaisance to a false definition of the term privateer Finding that the Jane had purchased new carriages to mount two or three additional guns which he had brought in her hold and that she opened additional port holes for them the carriages were ordered to be relanded the additional port holes stopped and her means of defence reduced to be the same at her departure as at her arrival This was done on the principle of allowing no party to arm within our ports."
By the way, notice the variant spellings (“shew” and “defence”). Writing at this time had lots of interesting variations. Be sure to plan to search for those alternates as well!
Finally, scanning through these texts, it’s a simple thing to find the letter of November 13, 1793, where Jefferson asserts that the Jane should be restored to her owners. It took a few months, but the Jane was found to NOT be a pirate, despite all of the armaments.
Search lessons: In this case I pursued two strategies in parallel. My search for an easily searchable full-text of Jefferson’s writings didn’t quite work out the way I’d hoped. But my more general search DID work, and I was able to find what I needed in Google Books… from the original 1793 printing.
Another key point to remember is that even relatively simple questions (“Was the Jane a pirate or not?”) often have richer, more complex answers than you might think. Jefferson’s choice was not just a simple yes/no determination of what the Jane’s intent was, but was played against a backdrop of a complex political situation that heavily influenced what judgments might be. Sometimes you just have to read a bit more than you’d think, just to understand what’s going on.
But that’s real research. And I find this kind of searching to be completely fascinating.