Note: On Aug 1, 2018 – כ״א אב תשע״ח, elevation became optionally available as a factor in most zmanim calculations. The KosherJava Zmanim library was updated to optionally allow using elevation as an attribute that will adjust most zmanim via the ZmanimCalendar.setUseElevation(boolean). There are some zmanim such as degree-based zmanim that are driven by the amount of light in the sky and are not impacted by elevation. These zmanim intentionally do not support elevation adjustment. The following is the original post.
I have received a few emails over the past year or so about the use of elevation as part of the calculation of various zmanim in the API. All releases of the zmanim API up to the current 1.1 release, use elevation to affect the calculation of all sunrise/sunset based zmanim. While my footnote on the Zmanim Calendar Generator page stated that this only impacted sunrise and sunset (quoting the Yisrael Vehazmanim and Calendrical Calculations), in practice all zmanim calculated based on sunrise and sunset were affected by elevation. An example of a zman that used elevation in 1.1, but will no longer in 1.2, is the calculation of Sof Zman Krias Shema according to the GR”A. The soon to be released version 1.2 limits the impact of elevation to sunrise and sunset only. The Zmanim Calendar Generator page already uses the latest changes to the code. To facilitate changes by ports of the API, a list of changes to the source code of the ZmanimCalendar.java and ComplexZmanimCalendar.java is available in a diff file (a proper Unix diff/patch is not available at this time). The diff files were generated prior to updating the JavaDocs to simplify the work of anyone modifying ports of the Zmanim API. Detailed sources for not using elevation for anything besides sunrise and sunset can be found in פרק ב׳ סעיף ט׳ (pages 186-187) in the second edition of Zmanim Kehilchasam זמנים כהלכתם by Rabbi Dovid Yehuda Bursztyn.