"Government, like dress, is the badge of lost innocence..."
See in text (I. Of the Origin and Design of Government in General, with Concise Remarks on the English Constitution)
This functions as both a simile and an allusion to the Bible. In the Garden of Eden, before Eve ate the apple, both she and Adam were nude, but after their collective loss of innocence they put on clothes as did all subsequent generations. With this comparison Paine is stating that government obscures what is pure, and is built upon a community's lost innocence.
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See in text (II. Of Monarchy and Hereditary Succession)
This indicates a structural shift in the text, wherein Paine goes on to describe passages of the Bible and how they serve as allusions to the present state of government affairs within the colonies. The Bible was an integral text during this period, particularly when it came to developing moral codes, which is why Paine alludes to it so heavily.
See in text (III. Thoughts on the Present State of American Affairs)
In Judeo-Christian ideology, Lucifer is an alternate name for the devil. Within this context, Paine is making a strong stance by equating anyone who promotes governmental discord to the devil.