* changed direct access of timestamp field to use getTimstamp() instead inside of calculateElapsedTime.

* Added support to the tomcat Server adaptor for correctly getting request start time. (Includes additional dependency on tomcat-coyote)
* Update layouts.html to document the addition of elapsedTime/D to the pattern support for IAccessEvent
* Modified AccessEvent.java to calculate the elapsedTime at construction of the event, instead of repeatedly in the getter.  This allows the value to be more easily seen in a debugger, and cleans up the code slightly.

Modified the regex patterns in RootCauseFirstThrowableProxyTest and
ExtendedThrowableProxyTest to find any packaging info in the throwable's
stack trace, including inexact matches.

On Cloudbees Jenkins, these tests were failing because they were looking
for an exact match of the JUnit package but only found an inexact one.

debug improvements to Gaffer

(cherry picked from commit bd88d3ed580a4f60dc54c3293eb42aee5ea73148)

Fix exception for logger name with '.' and '$'

LOGBACK-384 - Mixing periods and dollar signs in a logger
name causes IllegalArgumentException from LoggerFactory.getLogger

Fixing the logic to treat '$' and '.' at same level as per
comment [1]. Also adding a testcase

[1] http://jira.qos.ch/browse/LOGBACK-384?focusedCommentId=13105&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-13105

Use append instead of concatenate

Avoid NPE during JNDI lookup

Fixed an issue where an extra line of the stack trace was being printed by the ThrowableProxyConverter when specifying a length option.

The DataSourceConnectionSource.start() method opens a new connection
only to determine whether or not the discoverConnectionProperties()
should be called. This is unnecessary since that method will perform
the same check and issue a very similar warning. A more serious
problem is that the connection is never closed.

This commit removes the use of this extra connection completely. I
think this is the last issue in need of a fix before LOGBACK-376 can
be closed.

Use append instead of concatenate

Avoid NPE during JNDI lookup

LBCORE-179: Fix regarding incorrect stack trace depth when specifying %throwable with argument

Fixed JNDI lookup of non-String entries

Fixed MySQL setup script to use lower-case table name to match the references in the file. This had caused an error on systems where case sensitivity matters.

Removes redundant and forever dangling connection

Wrapped the call to System.getProperty in a try/catch to anticipate
the SecurityException that can result from accessing system properties
in the presence of a SecurityManager (e.g. in an applet sandbox).

Avoid NPE when getting CodeSource