Detect changed lines when running analysis in git submodules

Git submodules

Git Submodules feature allows to aggregate several Git repositories in a single one:
http://www.git-scm.com/book/en/v2/Git-Tools-Submodules

/myproject
    .git
    .gitmodules
    src1/
        .git
        foo.php
    src2/
        .git
        foo2.php

 Problem

The SonarQube scanner uses git to collect information: blame for each line, changed files/lines, merge bases, etc. Its current implementation, using JGit, doesn't support repositories using submodules. If the scanner runs in a project using git submodules, the behavior is undefined and it may result in wrong "new code" in pull requests or missing blame information.

The scanner should support analyzing a submodule in the same way as it's currently done when a project without submodules is analyzed.