There is a newly printed book entitled שורשי המצות לרמח׳ל claiming to be from a never before published manuscript from Rabbi Moshe Chaim Luzzato.
Does anyone know more about the discovery of this lost manuscript and where it turned up?
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The entire sefer can be read here for free (as Otzar HaChochmah now allows up to 150 pages of free viewing in each sefer, and this one is less than 150 pages).
On p. 5 it says the person who published the sefer (whom I'll call the publisher) expresses their thanks to the Jewish Theological Seminary for providing access to the manuscript, which is in their possession, so that it can be printed.
The publisher classifies this manuscript as MS 8339. On p. 7 the publisher says that marked on the manuscript are the words מחבר משוער רמח"ל, which I guess means it's estimated to be written by the Ramchal, but it's not guaranteed. However, the publisher says that after reading it, it's guaranteed to be from the Ramchal. Even though this is the publisher's opinion, they didn't want you to take their word for it, so they wrote on the cover מיסודו של הרמח"ל, not definitively writing that he was the author, and the reader will determine for themselves if the writing style proves the Ramchal wrote it.
The publisher adds that this manuscript is a Spanish (?, they write ספרדי) manuscript, and the copyist made a lot of typos. The manuscript itself has a lot of smudges as well, requiring best guesses what words were intended.
On p. 10 the publisher admits that this manuscript didn't have a name, but JTS classified it with the title שרשי המצות, and the publisher felt the title was appropriate.
The publisher didn't provide any other details as to the origin of this manuscript, other than that they found it due to "tremendous hashgacha pratis". I'll see if I can find any other historical details.
Edit: I found the manuscript online at the JTS library website, for those who want to see it. It was digitized onto the internet by hebrewbooks.org, by someone named Chaim in 2010. I couldn't find any mention that it is estimated to be written by the Ramchal, just that they say it's a 19th century manuscript of Kabbalah. There's also no mention of it being from a ספרדי copyist, so I don't know if that's the publisher's own evaluation (see there where they say there's typos based on havara), or JTS told them orally.