Cleanup of "using stan::math::x" and "using stan::x" for non-ambiguous functions

[rok-cesnovar]

Summary

This is another slam-dunkish PR to cleanup some of the old issues. I am running some performance/tuning tests and have some downtime to go through this easy stuff.

This PR removes the using statements for the following non-ambiguous functions:

stan::math::dot_self;
stan::math::include_summand;
stan::math::inv_logit;
stan::math::value_of;
stan::math::check_consistent_sizes;
stan::math::check_finite;
stan::math::check_not_nan;
stan::math::check_positive;
stan::math::check_less_or_equal;
stan::math::check_nonnegative;
stan::math::dot_product;
stan::math::square;

stan::is_constant_struct;
stan::is_vector;

The remaining using statements in stan/math are either in the Eigen namespace or for the following

functions 
max_size
get
length
is_vector
round
lgamma

Tests

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Side Effects

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Checklist

• Math issue Remove stan:: namespace qualification #594 and Remove unnecessary using statements from vectorized functions #426

• Copyright holder: Rok Češnovar, Univ. of Ljubljana

• the basic tests are passing

• the code is written in idiomatic C++ and changes are documented in the doxygen

• the new changes are tested

[syclik]

Sweet!

[rok-cesnovar]

I am getting the following error on the Windows jenkins machine. I tried restarting the Always-run tests part 1 but no dice :/

[main] make 17312 fork: child -1 - CreateProcessW failed for 'c:\Rtools\bin\make.exe', errno 30

make: make/compiler_flags:40: fork: Read-only file system