failOnAllIssues="true" is a blanket setting that enables failing on all issue types. It is not meant to be overridden by more fine-grained failOn* settings; the --do-not-fail-on-* CLI options are the intended mechanism for carve-outs. This works as designed (see #6829).

However, when failOnAllIssues="true" is configured together with an explicitly disabled fine-grained setting such as failOnSelfDeprecation="false", the fine-grained setting is silently ignored. A test runner warning should be emitted for this combination so that the conflict is no longer silent.

Proposed behavior

Given this XML configuration:

<phpunit failOnAllIssues="true"
         failOnSelfDeprecation="false">

a test runner warning such as this should be emitted:

failOnSelfDeprecation="false" has no effect because failOnAllIssues is enabled; use the --do-not-fail-on-self-deprecation CLI option to not fail on self-deprecations

The warning should be emitted for each fine-grained failOn* attribute that is explicitly set to false in the XML configuration file while failOnAllIssues is enabled (whether via the XML configuration file or via the --fail-on-all-issues CLI option).