It does not repeal the Act of 1779. As a matter of fact, it explicitly refers to it here:
"all persons not being natives, who have obtained a right to citizenship under the act entitled "An Act declaring who shall be deemed citizens of this Commonwealth".
This is referring to the 1779 act written by Thomas Jefferson, and that is it's actual title. Furthermore, depending on how the semicolon is intended, it may very well utilize the subsequent sentence as a descriptor of the preceding sentence.
"1. When two independent clauses are relatively short and the relationship between them (contrast, addition, cause, effect etc.) can be inferred without the coordinating conjunction, some writers find it more sophisticated to omit the coordinating conjunction and replace the comma with a semicolon. Not over-stressing the logical relationships and letting the reader infer them is a stylistic technique that advanced writers sometimes use.
In other words, all free persons born within the territory of this Commonwealth may be described by reference to "An Act declaring who shall be deemed citizens of this Commonwealth" 1779.
Your argument begs the obvious question. Unless the subsequent sentence describes the first, it serves no purpose. But if this were the case, why include the subsequent reference to the 1779 act at all? The fact that it is included means that it is relevant.
Even if your argument is correct, and jus soli interpretation has been added along with the 1779 jus sanguinus act, then it represents an augmentation and not a repeal.
In any case, it contains this caution: " Whereas it is the policy of all infant states to encourage a population, among other means an easy mode of admission to the rights of citizenship; yet wisdom and safety suggest the propriety of guarding against the introduction of secret enemies and of keeping the offices of government in the hands of citizens intimately acquainted with the spirit of the constitution and the genius of the people as well as permanently attached to the common interest:"
Seems as though the primary consideration and requirement of the entire act is to make citizenship easy to obtain for those people intent upon coming to the commonwealth to live as citizens. Exactly the same thing required in the "Naturalization act of 1790." It accepts foreign born, or born to foreign with the stipulation that they must become citizens.
That doesn't make any sense. The first sentence refers to those "born within the territory," and the second refers to "all persons, not being natives." The two sentences describe two different groups.
But if this were the case, why include the subsequent reference to the 1779 act at all? The fact that it is included means that it is relevant.
Simply to state that those who were already made citizens would still be citizens.