Input files all use UTF-8 encoding, need to read them that way

[jar398]

In Java, if the encoding is left unspecified, it does not default to UTF-8. You have to use an InputStreamReader song and dance to ensure that files are read properly. This is the cause of OpenTreeOfLife/reference-taxonomy#317 . The problem has been fixed in taxomachine, but needs tending to in treemachine as well.

Places that need changing:

src/main/java/opentree/GraphImporter.java:            BufferedReader br = new BufferedReader(new FileReader(filename));
src/main/java/opentree/IngestSynthesisData.java:            BufferedReader br = new BufferedReader(new FileReader(newickFile));
src/main/java/opentree/IngestSynthesisData.java:            BufferedReader br = new BufferedReader(new FileReader(fileName));
src/main/java/opentree/IngestSynthesisData.java:            FileReader fileReader = new FileReader(fileName);
src/main/java/opentree/IngestSynthesisData.java:            BufferedReader br = new BufferedReader(new FileReader(fileName));
src/main/java/opentree/IngestSynthesisData.java:            BufferedReader br = new BufferedReader(new FileReader(fileName));
src/main/java/opentree/MainRunner.java:            FileReader fileReader = new FileReader(jsonFile);
src/main/java/opentree/MainRunner.java:            BufferedReader br = new BufferedReader(new FileReader(taxonomyfile));
src/main/java/opentree/MainRunner.java:            BufferedReader br = new BufferedReader(new FileReader(filename));
src/main/java/opentree/MainRunner.java:            BufferedReader br = new BufferedReader(new FileReader(newickFile));

[jar398]

This also applies to ot-base.