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what does the term "well regulated" mean then?

Here is a breakdown of that specific part of the wording of the 2nd Amendment from GunCite.com...

Well Regulated

The Random House College Dictionary (1980) gives four definitions for the word "regulate," which were all in use during the Colonial period and one more definition dating from 1690 (Oxford English Dictionary, 2nd Edition, 1989). They are:

1) To control or direct by a rule, principle, method, etc.
2) To adjust to some standard or requirement as for amount, degree, etc.
3) To adjust so as to ensure accuracy of operation.
4) To put in good order.

[obsolete sense]
b. Of troops: Properly disciplined. Obs. rare-1.
1690 Lond. Gaz. No. 2568/3 We hear likewise that the French are in a great Allarm in Dauphine and Bresse, not having at present 1500 Men of regulated Troops on that side.

We can begin to deduce what well-regulated meant from Alexander Hamilton's words in Federalist Paper No. 29:

The project of disciplining all the militia of the United States is as futile as it would be injurious if it were capable of being carried into execution. A tolerable expertness in military movements is a business that requires time and practice. It is not a day, nor a week nor even a month, that will suffice for the attainment of it. To oblige the great body of the yeomanry and of the other classes of the citizens to be under arms for the purpose of going through military exercises and evolutions, as often as might be necessary to acquire the degree of perfection which would entitle them to the character of a well regulated militia, would be a real grievance to the people and a serious public inconvenience and loss.
--- The Federalist Papers, No. 29.

Hamilton indicates a well-regulated militia is a state of preparedness obtained after rigorous and persistent training. Note the use of 'disciplining' which indicates discipline could be synonymous with well-trained.

This quote from the Journals of the Continental Congress, 1774-1789 also conveys the meaning of well regulated:

Resolved , That this appointment be conferred on experienced and vigilant general officers, who are acquainted with whatever relates to the general economy, manoeuvres and discipline of a well regulated army.
--- Saturday, December 13, 1777.

In the passage that follows, do you think the U.S. government was concerned because the Creek Indians' tribal regulations were superior to those of the Wabash or was it because they represented a better trained and disciplined fighting force?

That the strength of the Wabash Indians who were principally the object of the resolve of the 21st of July 1787, and the strength of the Creek Indians is very different. That the said Creeks are not only greatly superior in numbers but are more united, better regulated, and headed by a man whose talents appear to have fixed him in their confidence. That from the view of the object your Secretary has been able to take he conceives that the only effectual mode of acting against the said Creeks in case they should persist in their hostilities would be by making an invasion of their country with a powerful body of well regulated troops always ready to combat and able to defeat any combination of force the said Creeks could oppose and to destroy their towns and provisions.
--- Saturday, December 13, 1777.

I am unacquainted with the extent of your works, and consequently ignorant of the number or men necessary to man them. If your present numbers should be insufficient for that purpose, I would then by all means advise your making up the deficiency out of the best regulated militia that can be got.
--- George Washington (The Writings of George Washington, pp. 503-4, (G.P. Putnam & Sons, pub.)(1889))

The above quote is clearly not a request for a militia with the best set of regulations. (For brevity the entire passage is not shown and this quote should not be construed to imply Washington favored militias, in fact he thought little of them, as the full passage indicates.)

But Dr Sir I am Afraid it would blunt the keen edge they have at present which might be keept sharp for the Shawnese &c: I am convinced it would be Attended by considerable desertions. And perhaps raise a Spirit of Discontent not easily Queld amongst the best regulated troops, but much more so amongst men unused to the Yoak of Military Discipline.
--- Letter from Colonel William Fleming to Col. Adam Stephen, Oct 8, 1774, pp. 237-8. (Documentary History of Dunmore's War, 1774, Wisconsin historical society, pub. (1905))

And finally, a late-17th century comparison between the behavior of a large collection of seahorses and well-regulated soldiers:

One of the Seamen that had formerly made a Greenland Voyage for Whale-Fishing, told us that in that country he had seen very great Troops of those Sea-Horses ranging upon Land, sometimes three or four hundred in a Troop: Their great desire, he says, is to roost themselves on Land in the Warm Sun; and Whilst they sleep, they apppoint one to stand Centinel, and watch a certain time; and when that time's expir'd, another takes his place of Watching, and the first Centinel goes to sleep, &c. observing the strict Discipline, as a Body of Well-regulated Troops
--- (Letters written from New-England, A. D. 1686. P. 47, John Dutton (1867))

The quoted passages support the idea that a well-regulated militia was synonymous with one that was thoroughly trained and disciplined, and as a result, well-functioning. That description fits most closely with the "to put in good order" definition supplied by the Random House dictionary. The Oxford dictionary's definition also appears to fit if one considers discipline in a military context to include or imply well-trained.

What about the Amendment's text itself? Considering the adjective "well" and the context of the militia clause, which is more likely to ensure the security of a free state, a militia governed by numerous laws (or the proper amount of regulation [depending on the meaning of "well"] ) or a well-disciplined and trained militia? This brief textual analysis also suggests "to put in good order" is the correct interpretation of well regulated, signifying a well disciplined, trained, and functioning militia.

And finally, when regulated is used as an adjective, its meaning varies depending on the noun its modifying and of course the context. For example: well regulated liberty (properly controlled), regulated rifle (adjusted for accuracy), and regulated commerce (governed by regulations) all express a different meaning for regulated. This is by no means unusual, just as the word, bear, conveys a different meaning depending on the word it modifies: bear arms, bear fruit, and bear gifts.