#53 ILoggingTool patch to make log4j optional

[Egon Willighagen]

This patch introduces a new LoggingTool framework, making the log4j-based implementation optional. It:

• introduces ILoggingTool
• introduces a LoggingToolFactory to instantiate a logger
• makes the log4j LoggingTool optional, and now available from the log4j module
• introduces a SystemOutLoggingTool for logging to STDOUT
• allows registration of custom ILoggingTool implementation with the LoggingToolFactory, with an example in the unit test class

The patch was written against master, and can be applied with 'git am'.

[Egon Willighagen]

Gziped tar file with 7 patches to be applied with 'git am'.

[Rajarshi Guha]

Patch 1 worked fine, but patch 2 fails on latest master

....
import java.util.List;
error: patch failed: build.xml:985
error: build.xml: patch does not apply
warning: src/main/org/openscience/cdk/config/ElementPTFactory.java has type 100755, expected 100644
error: patch failed: src/main/org/openscience/cdk/fingerprint/Fingerprinter.java:36
error: src/main/org/openscience/cdk/fingerprint/Fingerprinter.java: patch does not apply
error: patch failed: src/main/org/openscience/cdk/fingerprint/MACCSFingerprinter.java:68
error: src/main/org/openscience/cdk/fingerprint/MACCSFingerprinter.java: patch does not apply
....

[Egon Willighagen]

Rajarshi,

please find the patch rebased on the current master at:

http://github.com/egonw/cdk/tree/53-ILogger

[Rajarshi Guha]

Patches look good.Applied to master and pushed