--charset doesn't work for stdin

The compiler always reads stdin as UTF-8, regardless of `--charset`.

```bash
$ echo "var foo = '⌘';" | enconv -L none -x UCS-4 > test.js
$ java -jar compiler.js --charset=UTF-32 test.js # good
var foo="#";
$ java -jar compiler.js --charset=UTF-32 < test.js # bad
stdin:1: ERROR - Parse error. Character '' (U+0000) is not a valid identifier start char
var foo = '#';
^

1 error(s), 0 warning(s)
```

(Ignore the actual output. Not all characters came through in the paste. And note that UCS-4 and UTF-32 are synonyms.)

---

While fixing this, I deprecated the `SourceFile#fromInputStream` methods in favor of ones that accept `Charset`s.
It looks like this one isn't called anywhere, so we can actually delete it. The other deprecated one is actually called in some places so we'll need to leave it there for now.