Fix includes for Stan Math /prim flatten

[rok-cesnovar]

Submisison Checklist

• Run tests: ./runCmdStanTests.py src/test
• Declare copyright holder and open-source license: see below

Summary:

stan-dev/math#1606 will remove mat, arr and scal from the Stan Math's /prim folder. This PR fixes one include in the Cmdstan repo.

Copyright and Licensing

Please list the copyright holder for the work you are submitting (this will be you or your assignee, such as a university or company):
Rok Češnovar

By submitting this pull request, the copyright holder is agreeing to license the submitted work under the following licenses:

• Code: BSD 3-clause (https://opensource.org/licenses/BSD-3-Clause)
• Documentation: CC-BY 4.0 (https://creativecommons.org/licenses/by/4.0/)

[rok-cesnovar]

This PR should be merged together with #792 and stan-dev/stan#2876

[stan-buildbot]

---

Name	Old Result	New Result	Ratio	Performance change( 1 - new / old )
gp_pois_regr/gp_pois_regr.stan	4.87	4.85	1.0	0.49% faster
low_dim_corr_gauss/low_dim_corr_gauss.stan	0.02	0.02	0.97	-3.43% slower
eight_schools/eight_schools.stan	0.09	0.1	0.95	-5.04% slower
gp_regr/gp_regr.stan	0.22	0.22	1.01	1.22% faster
irt_2pl/irt_2pl.stan	6.07	6.06	1.0	0.17% faster
performance.compilation	87.82	86.95	1.01	0.99% faster
low_dim_gauss_mix_collapse/low_dim_gauss_mix_collapse.stan	7.35	7.33	1.0	0.25% faster
pkpd/one_comp_mm_elim_abs.stan	21.96	20.15	1.09	8.28% faster
sir/sir.stan	99.4	95.72	1.04	3.69% faster
gp_regr/gen_gp_data.stan	0.04	0.05	0.98	-1.65% slower
low_dim_gauss_mix/low_dim_gauss_mix.stan	2.96	2.95	1.0	0.12% faster
pkpd/sim_one_comp_mm_elim_abs.stan	0.35	0.32	1.12	10.64% faster
arK/arK.stan	2.43	2.41	1.01	0.51% faster
arma/arma.stan	0.79	0.79	1.0	0.08% faster
garch/garch.stan	0.52	0.6	0.88	-13.45% slower
Mean result: 1.00469648573

---

Jenkins Console Log
Blue Ocean
Commit hash: 54da5ef

---

Machine information

ProductName: Mac OS X ProductVersion: 10.11.6 BuildVersion: 15G22010

CPU:
Intel(R) Xeon(R) CPU E5-1680 v2 @ 3.00GHz

G++:
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 7.0.2 (clang-700.1.81)
Target: x86_64-apple-darwin15.6.0
Thread model: posix

Clang:
Apple LLVM version 7.0.2 (clang-700.1.81)
Target: x86_64-apple-darwin15.6.0
Thread model: posix

[stan-buildbot]

---

Name	Old Result	New Result	Ratio	Performance change( 1 - new / old )
gp_pois_regr/gp_pois_regr.stan	4.88	4.96	0.98	-1.69% slower
low_dim_corr_gauss/low_dim_corr_gauss.stan	0.02	0.02	0.96	-4.47% slower
eight_schools/eight_schools.stan	0.09	0.1	0.98	-2.5% slower
gp_regr/gp_regr.stan	0.22	0.22	1.0	0.11% faster
irt_2pl/irt_2pl.stan	6.08	6.09	1.0	-0.17% slower
performance.compilation	89.07	86.71	1.03	2.66% faster
low_dim_gauss_mix_collapse/low_dim_gauss_mix_collapse.stan	7.32	7.32	1.0	-0.05% slower
pkpd/one_comp_mm_elim_abs.stan	21.87	21.16	1.03	3.24% faster
sir/sir.stan	98.48	96.28	1.02	2.24% faster
gp_regr/gen_gp_data.stan	0.05	0.05	1.03	2.79% faster
low_dim_gauss_mix/low_dim_gauss_mix.stan	2.95	2.96	1.0	-0.18% slower
pkpd/sim_one_comp_mm_elim_abs.stan	0.32	0.32	1.0	-0.5% slower
arK/arK.stan	2.43	2.42	1.0	0.21% faster
arma/arma.stan	0.79	0.79	1.0	-0.08% slower
garch/garch.stan	0.52	0.59	0.88	-13.8% slower
Mean result: 0.993394740091

---

Jenkins Console Log
Blue Ocean
Commit hash: 54da5ef

---

Machine information

ProductName: Mac OS X ProductVersion: 10.11.6 BuildVersion: 15G22010

CPU:
Intel(R) Xeon(R) CPU E5-1680 v2 @ 3.00GHz

G++:
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 7.0.2 (clang-700.1.81)
Target: x86_64-apple-darwin15.6.0
Thread model: posix

Clang:
Apple LLVM version 7.0.2 (clang-700.1.81)
Target: x86_64-apple-darwin15.6.0
Thread model: posix

[mcol]

I hope it's fine for me to approve this in cmdstan. It'll have to wait for stan-dev/math#1606 to be merged.

[rok-cesnovar]

You have the permissions and understand the changes made, so I think its totally fine. Thanks by the way!

[stan-buildbot]

---

Name	Old Result	New Result	Ratio	Performance change( 1 - new / old )
gp_pois_regr/gp_pois_regr.stan	4.87	4.94	0.99	-1.34% slower
low_dim_corr_gauss/low_dim_corr_gauss.stan	0.02	0.02	0.99	-1.09% slower
eight_schools/eight_schools.stan	0.09	0.09	1.05	4.64% faster
gp_regr/gp_regr.stan	0.22	0.22	0.98	-1.62% slower
irt_2pl/irt_2pl.stan	6.06	6.08	1.0	-0.32% slower
performance.compilation	87.62	86.68	1.01	1.07% faster
low_dim_gauss_mix_collapse/low_dim_gauss_mix_collapse.stan	7.34	7.35	1.0	-0.16% slower
pkpd/one_comp_mm_elim_abs.stan	20.4	21.07	0.97	-3.27% slower
sir/sir.stan	102.98	104.07	0.99	-1.06% slower
gp_regr/gen_gp_data.stan	0.04	0.04	1.01	0.62% faster
low_dim_gauss_mix/low_dim_gauss_mix.stan	2.97	2.96	1.0	0.18% faster
pkpd/sim_one_comp_mm_elim_abs.stan	0.31	0.31	1.0	0.05% faster
arK/arK.stan	1.77	1.76	1.01	0.69% faster
arma/arma.stan	0.83	0.79	1.06	5.46% faster
garch/garch.stan	0.59	0.59	1.01	1.05% faster
Mean result: 1.00376380382

---

Jenkins Console Log
Blue Ocean
Commit hash: 54da5ef

---

Machine information

ProductName: Mac OS X ProductVersion: 10.11.6 BuildVersion: 15G22010

CPU:
Intel(R) Xeon(R) CPU E5-1680 v2 @ 3.00GHz

G++:
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1
Apple LLVM version 7.0.2 (clang-700.1.81)
Target: x86_64-apple-darwin15.6.0
Thread model: posix

Clang:
Apple LLVM version 7.0.2 (clang-700.1.81)
Target: x86_64-apple-darwin15.6.0
Thread model: posix