In the original editions of the Vulgate, were the apocryphal books separated?
The original Vulgate produced by Jerome around 382 has been lost to history, but texts of the Vulgate have been preserved in numerous manuscripts, albeit with many textual variants.
The Vulgate is largely the work of Jerome who, in 382, had been commissioned by Pope Damasus I to revise the Vetus Latina Gospels used by the Roman Church. Later, on his own initiative, Jerome extended this work of revision and translation to include most of the books of the Bible. The Vulgate became progressively adopted as the Bible text within the Western Church. Over succeeding centuries, it eventually eclipsed the Vetus Latina. By the 13th century it had taken over from the former version the designation versio vulgata (the "version commonly used") or vulgata for short. The Vulgate also contains some Vetus Latina translations that Jerome did not work on. Vulgate
Our modern biblical canon was more or less finalized in 350 at Jerusalem by Bishop Cyril of Jerusalem. Prior to that Both Irenaeus (in 160) and Origen (early 3rd century) had their own lists.
A four gospel canon (the Tetramorph) was in place by the time of Irenaeus, c. 160, who refers to it directly. By the early 200s, Origen may have been using the same 27 books as in the modern New Testament, though there were still disputes over the canonicity of Hebrews, James, II Peter, II and III John, and Revelation. Likewise, by 200 C.E., the Muratorian fragment shows that there existed a set of Christian writings somewhat similar to what is now the New Testament, which included the four gospels and argued against objections to them. Thus, while there was a good measure of debate in the Early Church over the New Testament canon, there were also precedents for the current canon dating back to the second century.
The canonical Christian Bible was formally established by Bishop Cyril of Jerusalem in 350 C.E., confirmed by the Council of Laodicea in 363 C.E., and later established by Athanasius of Alexandria in 367 C.E. In his Easter letter of 367 C.E., Athanasius, Bishop of Alexandria, gave a list of exactly the same books as what would become the New Testament canon, and he used the word "canonized" (kanonizomena) in regards to them. The African Synod of Hippo, in 393 C.E., approved the New Testament, as it stands today, together with the Septuagint books, a decision that was repeated by Councils of Carthage in 397 C.E. and 419 C.E. These councils were under the authority of Augustine of Hippo, who regarded the canon as already closed. Pope Damasus I's Council of Rome in 382 C.E., if the Decretum Gelasianum is correctly associated with it, issued a biblical canon identical to that mentioned above, or if not the list is at least a sixth century compilation. Likewise, Damasus's commissioning of the Latin Vulgate edition of the Bible, c. 383, was instrumental in the fixation of the canon in the West. In 405, Pope Innocent I sent a list of the sacred books to a Gallic bishop, Exsuperius of Toulouse. When these bishops and councils spoke on the matter, however, they were not defining something new, but instead "were ratifying what had already become the mind of the Church." Thus, from the fourth century, there existed unanimity in the West concerning the New Testament canon (as it is today), and by the fifth century the East, Eastern Orthodoxy with a few exceptions, had come to accept the Book of Revelation and thus had come into harmony on the matter of the canon. Nonetheless, a full dogmatic articulation of the canon was not made until the Council of Trent of 1546 for Roman Catholicism, the Thirty-Nine Articles of 1563 for the Church of England, the Westminster Confession of Faith of 1647 for Calvinism, and the Synod of Jerusalem of 1672 for the Greek Orthodox. - Biblical canon
As for the Old Testament, the 4th century saw the Biblical canon set in the West.
For mainstream Pauline Christianity (growing from proto-orthodox Christianity in pre-Nicene times) which books constituted the Christian biblical canons of both the Old and New Testament was generally established by the 5th century, despite some scholarly disagreements, for the ancient undivided Church (the Catholic and Eastern Orthodox traditions, before the East–West Schism). The Catholic canon was set at the Council of Rome (382), the same Council commissioned Jerome to compile and translate those canonical texts into the Latin Vulgate Bible. In the wake of the Protestant Reformation, the Council of Trent (1546) affirmed the Vulgate as the official Catholic Bible in order to address changes Martin Luther made in his recently completed German translation which was based on the Hebrew language Tanakh in addition to the original Greek of the component texts. The canons of the Church of England and English Presbyterians were decided definitively by the Thirty-Nine Articles (1563) and the Westminster Confession of Faith (1647), respectively. The Synod of Jerusalem (1672) established additional canons that are widely accepted throughout the Orthodox Church.
Various forms of Jewish Christianity persisted until around the fifth century, and canonicalized very different sets of books, including Jewish–Christian gospels which have been lost to history. These and many other works are classified as New Testament apocrypha by Pauline denominations.
The Old and New Testament canons did not develop independently of each other and most primary sources for the canon specify both Old and New Testament books. For the biblical scripture for both Testaments, canonically accepted in major traditions of Christendom, see Biblical canon § Canons of various Christian traditions.
Council of Trent
In light of Martin Luther's demands, the Council of Trent on 8 April 1546 approved the present Catholic Bible canon, which includes the Deuterocanonical Books, and the decision was confirmed by an anathema by vote (24 yea, 15 nay, 16 abstain). The council confirming the same list as produced at the Council of Florence in 1442, Augustine's 397-419 Councils of Carthage, and probably Damasus' 382 Council of Rome. The Old Testament books that had been rejected by Luther were later termed deuterocanonical, not indicating a lesser degree of inspiration, but a later time of final approval. Beyond these books, the Sixto-Clementine Vulgate contained in the Appendix several books considered as apocryphal by the council: Prayer of Manasseh, 3 Esdras, and 4 Esdras. - Biblical canon
What books the original Vulgate of St. Jerome actually contained is an open question. But seeing that as St. Jerome died in 420 and that the Biblical Canon for the Church in the West was completed in 350, it would seem logical that the original Vulgate contained the Biblical Canonical books of the Old and New Testaments, as well as the deuterocanonical books. These books and passages are considered by the Catholic Church, the Eastern Orthodox Church, the Oriental Orthodox Churches, and/or the Assyrian Church of the East to be canonical books of the Old Testament, but which Jews and Protestant denominations regard as apocrypha. They date from 300 BC to 100 AD, mostly from 200 BC to 70 AD, before the definite separation of the Christian church from Judaism.
This stated, some editions of the Sixto-Clementine Vulgate has an appendage to the Bible as an added reading source of 3 Apocrypha in order that these books would no be lost to historical interest, lest they be forgotten (Numquam Obliviscamur). These books were usually the Prayer of Manasses, 1 Esdras and 2 Esdras. Other editions of the Vulgate vary in the Apocrypha, in the order of the books, and in the names of the books. I once had a Vulgate that also contained the Book of Enoch as an historical additional reading source.
These books were never part of the Catholic Biblical Canon, but were added at the end of certain Vulgate editions for educational reasons and biblical scholar's interests. The Sacred Scriptures make reference to these historical sources and it is in this light that the documents were placed at the end of some Catholic Vulgates for educators of the Sacred Scriptures.
It should be known that the term ”deuterocanonical” was etymologically in existence as 1684 and thus the bible of St. Jerome did not make any distinction between in its’ biblical Canon expect for those texts that the Church sees as ”Apocryphal”. Obviously, this was due to the Protestant influences in Church history!