--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.
I was unsure whether anyone using the Java API used this one.

e.g. `fromInputStream` is mentioned in "Closure: The Definitive Guide".

Are you sure it will be okay to remove?