Replaced log4j with java logging, removed OWLManager references

In order to fit this as a module for OWLAPI, references to OWLManager
need to exist only in the test packages.

OWLAPI uses java logging, so replacing log4j to avoid client code 
having to set up both logging systems.
This might be reverted later, as it's not clear yet whether OWLAPI
should stick with java logging or move to a different API.
removed deprecations

IRI.getStart() has been deprecated. Replaced with a simpler idiom.
URLDecoder.decode() should pass in the intended character encoding. This
should be UTF-8.
removed Log4J from test classes and added Java logging settings
refactored owl2obo and obo2owl to separate dependency on OWLManager
ignore target and mac specific files
synchronized with OWLAPI repo
sync with OWLAPI 3.4.10-SNAPSHOT
Synchronised with changes in OWLAPI 3.4.10
new

git-svn-id: http://oboformat.googlecode.com/svn/trunk@600 3e622410-f0ad-ce59-49ea-9bf623c22f00
* all synonyms require a type
* remove code which lead to a wrong synonym declaration for sub
annotation properties in owl2obo

Conflicts:
	src/main/java/org/obolibrary/obo2owl/Owl2Obo.java

git-svn-id: http://oboformat.googlecode.com/svn/trunk@601
3e622410-f0ad-ce59-49ea-9bf623c22f00
fix position of import tags in the OBO header, make it fully compatible
with OBO-Edit
Format code with OWLAPI style

Simplifies synchronizing changes
warning removed
new

git-svn-id: http://oboformat.googlecode.com/svn/trunk@603 3e622410-f0ad-ce59-49ea-9bf623c22f00
Made owl2obo robust in the face of axiom annotations whose values are
IRIs and not literals
new test, synonym annotations

git-svn-id: http://oboformat.googlecode.com/svn/trunk@606 3e622410-f0ad-ce59-49ea-9bf623c22f00
* sort order for trailing qualifier values (lexical as in OBO-Edit)
* try to preserve relationship tags in obo2owl roundtrips for
is_meta_data tag level relations (i.e. never_in_taxon)
* remove some dead code
* only try to translate to relationships for term frames
* fix test: set proper type for external links
add test case for labeled xrefs

git-svn-id: http://oboformat.googlecode.com/svn/trunk@609 3e622410-f0ad-ce59-49ea-9bf623c22f00
make oboformat 0.5.5 release