The word so is grammatically protean: it can be an adverb, an adjective, a conjunction, a pronoun, or an interjection. Its definition in standard dictionaries, including the online Oxford English Dictionary, stretches over many pages. But as to its  semantic range as an interjection, standard sources like The American Heritage Dictionary are incomplete, not having caught up with current usage, specifically in Geek (not to be confused with Greek), the language of computer geeks.

It has been remarked that geeks often begin discourses with so, typically in answer to a question but not only. In the latter case, the question is virtual and implied. This virtuality is rooted in the nature of computer science, where the interrogative mode reigns supreme: the milieu is suffused with an atmosphere of problems to be solved, i.e., with questions suspended in the air that geeks breathe (“How? Why? What if?,” etc.).

It is in this light that one can see why the discourse-introductory so has come to be a characteristic of the geek argot. It is a grammatical manifestation of what the French call déformation professionnelle.

The origin of this usage may be Yiddish. Considering the ethnic makeup of the mathematicians and scientists who played a role in the computer revolution’s intellectual history, this is not altogether unexpected. Here is some evidence for this claim from the online OED.

Consider one of the subsidiary entries for so:

10. a. For that reason, on that account, accordingly, consequently, therefore.
The causative force is sometimes very slight, the use approximating to that in b.

b. (a) As an introductory particle, without a preceding statement (but freq. implying one). 1710 SWIFT Jrnl. to Stella 21 Sept., So you have got into Presto’s lodgings; very fine, truly! 1777 SHERIDAN Sch. Scandal II. iii, Well, so one of my nephews is a wild rogue, hey? 1809 BYRON in R. C. Dallas Corr. of B. (1825) I. 95 So Lord G* is married to a rustic! Well done! 1881 JOWETT Thucyd. I. 42 And so we have met at last, but with what difficulty!

(b) [Reflecting Yiddish idioms.] Without implication of a preceding statement, or with concessive force: = well then, in that case, very well; also (introducing interrogative clauses) with adversative force: = but then, anyway. 1950 B. MALAMUD in Partisan Rev. XVII. 666 Miriam returned after 11.30… ‘So where did you go?’ Feld asked pleasantly. 1952 M. PEI Story of English 182 The adverb so at the beginning of a sentence (‘So I’ll pay for it!’), probably of Yiddish origin, occurs frequently in conversation. 1960 ‘E. MCBAIN Give Boys Great Big Hand i. 4 ‘I warn you..I ain’t got no wine.’ ‘So who wants wine?’ 1977 F. BRANSTON Up & Coming Man v. 49 ‘How much profit..?’ ‘Impossible to do more than make a wild guess.’ ‘So make a wild guess.’”

The trajectory from (Yiddish-)American “So where did you go?” and “So make a wild guess” to discourse-introductory Geek “So the program needs to be downloaded . . ., etc.” is a short and plausible one.