This may be intent rather than bug, but where I have a file with a class with > 90% test coverage, the file's "traits & classes" summary reports test coverage as 0%.

It's possible (but unconfirmed) that this is causing an issue with https://github.com/theseer/phpdox/issues/147, whereby all classes are being considered "untested".
Produced with https://github.com/parsingphase/enigma-simulator/tree/phpdox-no-coverage by running ant install-dev clean build
Installed versions on my system:
wechsler@tahr:~/host/repos/enigma-simulator$ composer show --installed
nikic/php-parser v1.0.0 A PHP parser written in PHP
ocramius/instantiator 1.1.3 A small, lightweight utility to instantiate objects in PHP without invoking their constructors
ocramius/lazy-map 1.0.0 A library that provides lazy instantiation logic for a map of objects
pdepend/pdepend 2.0.2 Official version of pdepend to be handled with Composer
phploc/phploc 2.0.6 A tool for quickly measuring the size of a PHP project.
phpmd/phpmd 2.1.3 Official version of PHPMD handled with Composer.
phpunit/php-code-coverage 2.0.11 Library that provides collection, processing, and rendering functionality for PHP code coverage information.
phpunit/php-file-iterator 1.3.4 FilterIterator implementation that filters files based on a list of suffixes.
phpunit/php-text-template 1.2.0 Simple template engine.
phpunit/php-timer 1.0.5 Utility class for timing
phpunit/php-token-stream 1.3.0 Wrapper around PHP's tokenizer extension.
phpunit/phpunit 4.2.6 The PHP Unit Testing framework.
phpunit/phpunit-mock-objects 2.2.1 Mock Object library for PHPUnit
sebastian/comparator 1.0.0 Provides the functionality to compare PHP values for equality
sebastian/diff 1.2.0 Diff implementation
sebastian/environment 1.0.0 Provides functionality to handle HHVM/PHP environments
sebastian/exporter 1.0.1 Provides the functionality to export PHP variables for visualization
sebastian/finder-facade 1.1.0 FinderFacade is a convenience wrapper for Symfony's Finder component.
sebastian/git 1.2.0 Simple wrapper for Git
sebastian/phpcpd 2.0.1 Copy/Paste Detector (CPD) for PHP code.
sebastian/version 1.0.3 Library that helps with managing the version number of Git-hosted PHP projects
squizlabs/php_codesniffer 1.5.5 PHP_CodeSniffer tokenises PHP, JavaScript and CSS files and detects violations of a defined set of coding standards.
symfony/config v2.5.5 Symfony Config Component
symfony/console v2.5.5 Symfony Console Component
symfony/dependency-injection v2.5.5 Symfony DependencyInjection Component
symfony/filesystem v2.5.5 Symfony Filesystem Component
symfony/finder v2.5.5 Symfony Finder Component
symfony/yaml v2.5.5 Symfony Yaml Component
theseer/directoryscanner 1.3.0 A recursive directory scanner and filter
theseer/fdomdocument 1.6.0 The classes contained within this repository extend the standard DOM to use exceptions at all occasions of errors instead of PHP warnings or notices. They al...
theseer/fxsl 1.1.0 An XSL wrapper / extension to the PHP 5.x XSLTProcessor with Exception and extended Callback support
theseer/phpdox dev-master 9392c5e A fast Documentation generator for PHP Code using standard technology (SRC, DOCBLOCK, XML and XSLT) with event based processing
This is intentional. Quoting from http://thephp.cc/dates/2014/international-php-conference-spring-edition/code-coverage-covered-in-depth
"PHP_CodeCoverage only considers a function or method as covered when all of its executable lines are covered. [...] PHP_CodeCoverage only considers a class or trait as covered when all of its methods are covered."
Thanks for clarifying :)
You're welcome. Wondering now whether we should add this information to the documentation.
Probably worth it for completeness? Checking the docs (https://phpunit.de/manual/current/en/code-coverage-analysis.html), I note that "Lines of code that were executed while running the tests are highlighted green" - but this appears to only apply to code executed by the test... methods themselves rather than code executed by dataProvider functions (executed in the ...Test classes but outside the test... methods). Again, quite possibly intended behaviour but an edge case in the docs and not 100% clear.
I just spent a good half hour confused by this as well.
Maybe the reports should clarify by using a better description, e.g. "Full Classes" rather than just "Classes"?
Also, I might want to know how many classes were _partially_ covered, so perhaps the results ought to include all three numbers? e.g. something like Classes: 0.00%~60.00% (0~3/5), which would at least prompt you to ask questions rather than making assumptions?
The information has been added to the documentation.
Most helpful comment
This is intentional. Quoting from http://thephp.cc/dates/2014/international-php-conference-spring-edition/code-coverage-covered-in-depth
"PHP_CodeCoverage only considers a function or method as covered when all of its executable lines are covered. [...] PHP_CodeCoverage only considers a class or trait as covered when all of its methods are covered."