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were out of date.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.
Added somewhat more complete gitignore.
Added site mechanics, initial Maven site and required plugins and settings to reactor root.
Parent poms pending.
Added local codestyle project, with option to include local enforcement rules.
Added new cobertura parent pom.
Added API parent.
Tmp commit; added annotations and metrics component structure.
Added simplified metrics model, as well as partial components for external interactions.
Updated metrics model to contain branch segments. Added initial Metrics API with coverage calculator and event listener specification.
Metrics API tmp addition of locations and tests.
Added coverage scope concept. Updated coverage calculator.
Normalized line endings.
Moved packages for the CoverageScope types.
Moved packages for the CoverageScope types.
Merge branch 'fixJaxbDependencies'
Ignore class annotations support added. Matched classes won't be instrumented