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I want to make my web application able to work offline and as soon as it becomes online or gets connected again, then it should be able to transfer the modifications made by user in offline mode.
I have seen Google Gears as an ideal solution for my problem, which is not recommended to be used as it is now deprecated.
What is a good way to make my application work offline, both in terms of technology to use and application design?
Gears is deprecated because the HTML5 standard allows for equivalent features to be present in compliant browsers.
With respect to your current problem at hand of handling offline web application access, you can look into the support offered by HTML5 for offline web applications via support for client-side SQL database access, and the client-side application HTTP cache.
The features will have to be used in conjunction, as the client-side database access will allow for storage of data (generated when the application is offline) in a structured format, while the offline application cache will allow for caching of HTTP responses from the server; you should not be caching responses that are dynamic in nature which depend on any user-provided inputs.
The details of the proposed APIs can be found in the W3C HTML5 specification, which is in draft at the moment, although it appears that certain user-agents have already implemented this feature.