On Linux, @atom/watcher uses inotify. Each watched directory is added to the watch list of a single inotify instance. Out-of-band command processing is triggered by writing to a pipe shared between the main and worker threads. The worker thread uses poll() to wait for either the command trigger or the inotify descriptor to become ready.
inotify cannot watch directories recursively. To watch directory trees, @atom/watcher creates new watch descriptors for each subdirectory added. There is a race condition here: events triggered between the subdirectory's creation and the worker thread processing it may occur before the subdirectory's watch descriptor is added, and so may be lost.
inotify uses a "cookie" field to correlate rename pairs. @atom/watcher attempts to correlate event cookies across consecutive event batches, but if two batches pass without a matching pair, the event is flushed as a creation or deletion instead.
Linux systems have a limited number of watch descriptors for each user. This limit is configurable and can vary from distro to distro; on Ubuntu, for example, it defaults to 8192. When watch descriptors are exhausted, @atom/watcher falls back to polling. Note that this can lead to odd situations where a watched subtree is partially watched by inotify and partially polled.