Java, like NT, was originally UCS-2 and moved to UTF-16 when it became clear that UCS-2 won't suffice. APIs that operate on units (anything involving "char"s [the type], CharSequences and so on) are legacy and, when used, are almost certainly used incorrectly. Note that newer APIs on String also use the word "char", but the type "int", these are actually operating on code points and not CUs, ie. these APIs are correct.

(Note that java.lang.Character is a char, so wrong. I think there is no CodePoint type or similar that wraps int.)

In Java regexps, the dot matches a code point or an unpaired surrogate, so if you have a proper surrogate pair, the dot matches the whole pair without splitting it. It does split grapheme clusters.

It's unclear to me what you mean by "Java Characters". A Java char is a UTF-16 code unit, and the java.lang.Character boxes a char (16 bits unsigned). However, since Java 5, java.lang.Character has static methods for astral-aware UTF-16 operations where a code point is a Java int (32 bits signed).