Remove bogus DTD declaration from web.xml

The web-app element requires version 2.4 of the Java Servlet specification
while the DTD points to version 2.3. This confuses some app servers and e.g.
GlassFish 3.1 reports the following error and refuses to deploy the
application:

Error occurred during deployment: Exception while deploying the app [coberturaFlush] : org.xml.sax.SAXParseException: Attribute "xmlns" must be declared for element type "web-app".. Please see server.log for more details.

I don't think there even is a DTD for version 2.4 anymore and removing the
2.3 DTD declaration fixes the issue.
Bring web.xml elements into correct order

The 2.4 web-app XML schema is strict about the order of some elements
in the web.xml. Put the elements into the correct order.
Remove duplicate web.xml file

The file that actually gets bundled is in src/main/resources.
Do not add dependencies to web app manifest classpath

No dependencies are needed except for cobertura.jar. The classpath manifest
entries will trigger errors like this when deploying to GlassFish 3.1:

|WARNING|glassfish3.1.1|org.apache.jasper.runtime.TldScanner|_ThreadID=24;_ThreadName=Thread-2;|PWC6351: In TLD scanning, the supplied resource file:/opt/glassfish3/glassfish/domains/domain1/applications/lib/hamcrest-core-1.3.jar does not exist
Created a static method that plugins can call that doesn't perform a System.exit
Add filtering of command-line scripts

The command-line scripts were modified to include tokens for the
versions of the different libraries, which will change over time and
were out of date. The modified POM now filters the scripts,
substituting in the versions as specified in the POM, and the modified
assembly descriptor includes them in the distribution.
Ignore class annotations support added. Matched classes won't be instrumented
Remove command-line scripts from JAR

The commit that added script filtering inadvertently allowed the
filtered scripts to be included in the Cobertura JAR. This commit
excludes them.
Fix issue #87, support final keyword in TryWithResources parsing
Merge pull request #158 from archmageirvine/master

Fix issue #87, support final keyword in TryWithResources parsing
Point to license file in license disclosure
Merge pull request #164 from streetlight/patch-1

Point to license file in license disclosure
Merge pull request #117 from kadim/master

Ignore class annotations support added. Matched classes won't be instrumented
Merge pull request #98 from stevesaliman/master

Created a static method that plugins can call that doesn't perform a Sys...
Merge pull request #102 from kbzod/scriptfilter

Use Maven filtering on command-line scripts to set versions properly
Add test unit for #170.
Add .gitignore rule for autogenerated code.
Add source code to html report for test units.
Remove Javac compiler and replace with built-in compiling option. This will allow users to build cobertura using their default jdk. We still neeed to keep this option in for compiling groovy code as we are unable to use the built-in compiler to copmile groovy code.
Cleaned up #170 a little.