bindings: update for sr_output_options_{get,free} API change.
Fix include paths for out-of-tree builds
Makefile.am: Fix doxygen invocation in out-of-tree build
Makefile.am: Fix out-of-tree build for C++ and Java bindings
configure.ac: Look for python-2.7.pc as well when making bindings
Makefile.am: Fix out-of-tree build for Python bindings
saleae-logic16: Recognize FPGA FIFO overflow status
unitests: Adapt to recent API changes.
output: Fix output option enumeration.
output: Fix double free.
input: s/format/module in all naming.
input: make sr_input{_module} opaque to clients.
input: Introduce new input module API.

This is a work in progress.
input: Fix up API documentation.
input: Fixes and VCD.
input: Frontends don't need to see SR_INPUT_META_*.
input: Actually return a NULL-terminated array.
input: Fix internal API docs.
input: Fix option enumeration.
input: sr_input_new() always allocates the instance buffer.