Separate sequential APIs and data structure + other updates to APIs

[lee30sonia]

• Some unused/duplicated APIs are deprecated: substitute_node_of_parents, num_latches (use num_registers instead), latch_reset.
• Added APIs register_at and set_register to retrieve and set register information. Remove the "reset" argument of create_ri.
• (important!) Networks do not provide sequential interfaces by default anymore. This simplifies the data structures and implementations. Sequential APIs can be extended to networks (that originally provides them) by wrapping the network with sequential, so the impact on existing code is little.
• Removed *_index APIs in klut_network and cover_network as they don't seem to be correctly implemented and also no test or algorithm actually use them.
• (This is more implementation detail): trav_id is moved from the custom storage data (e.g. aig_storage_data) to the common storage. num_pis and num_pos are moved to sequential_storage in sequential (because for combinational networks, these should be the same as the sizes of inputs and outputs vectors). As a result, custom storage data of some networks is removed when not needed (aig_storage_data, xag_storage_data, mig_storage_data, xmg_storage_data).
• Significant cleaning-up and sorting-out of the documentations related to APIs and networks.

As this PR makes significant changes, especially for the sequential APIs, I'm tagging anyone I know who may be affected or had contributed to related code in the history: @hriener @maustin8 @yashton @wlneto

[codecov-commenter]

Codecov Report

Merging #564 (94d892e) into master (6261bc5) will increase coverage by 0.07%. The diff coverage is 98.76%.

@@            Coverage Diff             @@
##           master     #564      +/-   ##
==========================================
+ Coverage   82.94%   83.02%   +0.07%     
==========================================
  Files         155      156       +1     
  Lines       19191    19085     -106     
==========================================
- Hits        15918    15845      -73     
+ Misses       3273     3240      -33     

Impacted Files	Coverage Δ
...de/mockturtle/algorithms/aqfp/aqfp_resynthesis.hpp	88.31% <ø> (+11.38%)	:arrow_up:
include/mockturtle/networks/storage.hpp	100.00% <ø> (ø)
include/mockturtle/views/immutable_view.hpp	100.00% <ø> (ø)
include/mockturtle/views/mapping_view.hpp	100.00% <ø> (ø)
include/mockturtle/views/window_view.hpp	100.00% <ø> (ø)
include/mockturtle/io/blif_reader.hpp	94.01% <93.33%> (-0.15%)	:arrow_down:
include/mockturtle/algorithms/node_resynthesis.hpp	84.48% <100.00%> (ø)
include/mockturtle/io/aiger_reader.hpp	98.38% <100.00%> (+0.14%)	:arrow_up:
include/mockturtle/io/serialize.hpp	89.00% <100.00%> (+1.50%)	:arrow_up:
include/mockturtle/io/write_aiger.hpp	84.21% <100.00%> (-0.41%)	:arrow_down:
... and 19 more

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