Makefiles: strip newlines in findiles and fix runChecks call

[rok-cesnovar]

Summary

Strips whitespace in findiles. The whitespaces created a lot of empty lines. See stan-dev/cmdstan#844

Also changes how we call runChecks.py
Reasons for the change are given here #1774 (comment)

Tests

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Side Effects

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Checklist

• Math issue No math issue - see Cleanup build warnings on Windows cmdstan#786

• Copyright holder: (fill in copyright holder information)

  The copyright holder is typically you or your assignee, such as a university or company. By submitting this pull request, the copyright holder is agreeing to the license the submitted work under the following licenses: Rok Češnovar
  - Code: BSD 3-clause (https://opensource.org/licenses/BSD-3-Clause)
  - Documentation: CC-BY 4.0 (https://creativecommons.org/licenses/by/4.0/)

• the basic tests are passing

  • unit tests pass (to run, use: ./runTests.py test/unit)
  • header checks pass, (make test-headers)
  • dependencies checks pass, (make test-math-dependencies)
  • docs build, (make doxygen)
  • code passes the built in C++ standards checks (make cpplint)

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

• the new changes are tested

[stan-buildbot]

---

Name	Old Result	New Result	Ratio	Performance change( 1 - new / old )
gp_pois_regr/gp_pois_regr.stan	4.9	4.91	1.0	-0.11% slower
low_dim_corr_gauss/low_dim_corr_gauss.stan	0.02	0.02	0.96	-3.97% slower
eight_schools/eight_schools.stan	0.09	0.09	1.02	2.02% faster
gp_regr/gp_regr.stan	0.22	0.22	1.0	-0.29% slower
irt_2pl/irt_2pl.stan	6.43	6.51	0.99	-1.15% slower
performance.compilation	88.0	86.59	1.02	1.61% faster
low_dim_gauss_mix_collapse/low_dim_gauss_mix_collapse.stan	7.54	7.51	1.0	0.42% faster
pkpd/one_comp_mm_elim_abs.stan	20.95	21.93	0.96	-4.67% slower
sir/sir.stan	91.01	91.98	0.99	-1.07% slower
gp_regr/gen_gp_data.stan	0.05	0.05	0.98	-2.24% slower
low_dim_gauss_mix/low_dim_gauss_mix.stan	2.98	2.95	1.01	0.75% faster
pkpd/sim_one_comp_mm_elim_abs.stan	0.32	0.31	1.03	2.52% faster
arK/arK.stan	1.74	1.76	0.99	-1.41% slower
arma/arma.stan	0.66	0.67	0.98	-2.35% slower
garch/garch.stan	0.51	0.52	1.0	-0.28% slower
Mean result: 0.993629064114

---

Jenkins Console Log
Blue Ocean
Commit hash: c73c8d8

---

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

[rok-cesnovar]

@mitzimorris mind reviewing this one when you have the chance? It will solve the issues in stan-dev/cmdstan#844

[mitzimorris]

lgtm!

[stan-buildbot]

---

Name	Old Result	New Result	Ratio	Performance change( 1 - new / old )
gp_pois_regr/gp_pois_regr.stan	4.89	4.88	1.0	0.38% faster
low_dim_corr_gauss/low_dim_corr_gauss.stan	0.02	0.02	1.01	1.43% faster
eight_schools/eight_schools.stan	0.09	0.09	1.03	2.83% faster
gp_regr/gp_regr.stan	0.22	0.22	1.01	0.62% faster
irt_2pl/irt_2pl.stan	6.45	6.44	1.0	0.07% faster
performance.compilation	87.87	86.41	1.02	1.66% faster
low_dim_gauss_mix_collapse/low_dim_gauss_mix_collapse.stan	7.54	7.59	0.99	-0.73% slower
pkpd/one_comp_mm_elim_abs.stan	20.35	20.35	1.0	-0.0% slower
sir/sir.stan	93.74	93.88	1.0	-0.15% slower
gp_regr/gen_gp_data.stan	0.05	0.05	1.02	1.8% faster
low_dim_gauss_mix/low_dim_gauss_mix.stan	2.95	3.15	0.94	-6.62% slower
pkpd/sim_one_comp_mm_elim_abs.stan	0.32	0.31	1.03	2.65% faster
arK/arK.stan	1.74	1.75	1.0	-0.38% slower
arma/arma.stan	0.67	0.67	1.0	0.29% faster
garch/garch.stan	0.51	0.51	1.0	0.43% faster
Mean result: 1.00328068839

---

Jenkins Console Log
Blue Ocean
Commit hash: abddcc0

---

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