When the same plugin directory is discovered through different path
representations (e.g. symlinks), the manifest registry incorrectly
warns about a duplicate plugin id. This is a false positive that
appears for bundled extensions like feishu (#16208).
Compare fs.realpathSync() of both candidates' rootDir before emitting
the duplicate warning. If they resolve to the same physical directory,
silently skip the duplicate instead of warning.
Also change seenIds from Set<string> to Map<string, PluginCandidate>
to track the first-seen candidate for comparison.
Closes#16208
