Enhancements to Simulation Timestamps and JSON output

[henricasanova]

• Add the file name to the "read" element of the JSON output (since the corresponding TimeStamp has the file)
• Add a DiskReadStart/End and DiskWriteStart/End TimeStamp, and generate them in S4U_Simulation.cpp (see "TODO" comments therein)
• Add a "disks" section to the JSON with data from the above timestamp (num bytes, host, disk path)
• Enhance the SimulationOutput API so that one must enable various "categories" of time-stamps.
• Make sure Doxygen document for all the "dump JSON" methods is up-to-date

[willkoch]

File IDs added to read/write

[henricasanova]

Modified the API so that timestamp constructors are now private, and instead a number of addTimestamp...() methods have been added to SimulationOutput. After tinkering with heavily templated complicated design, went for simple.

New methods added to enable/disable timestamp generation at the user-level. By default, all currently available timestamps are enabled, but likely the upcoming disk-related timestamps will not. Look in the constructor SimulationOutput::SimulationOutput() where the default enabled/disabled statuses are set.

[willkoch]

Timestamps implemented (with wrapper in Simulation.cpp instead of S4U_Simulation.cpp) and JSON added for disk specific output. Disk timestamps disabled by default

[willkoch]

Fixed formatting for all dumps. Closing now, not yet reflected on the website.