model$format and model$check_syntax fail to account for include-paths on compiled models

[adrian-lison]

Describe the bug
The new format method is really nice! However, I noticed that it fails to account for include paths when applied to CmdStanModel objects that were already compiled. The same applies to the check_syntax method (if include-paths is not explicitly supplied).

To Reproduce
Just take the corresponding testthat test, which originally only tests an uncompiled model and run it with a compiled model:

  stan_program_w_include <- testing_stan_file("bernoulli_include")

  mod_w_include <- cmdstan_model(stan_file = stan_program_w_include, compile=TRUE,
                                   include_paths = test_path("resources", "stan"))
  expect_output(
    mod_w_include$format(),
    "#include ",
    fixed = TRUE
  )
  expect_output(
    mod_w_include$format(canonicalize = list('deprecations', 'parentheses', 'braces')),
    "#include ",
    fixed = TRUE
  )
    expect_output(
    mod_w_include$format(canonicalize = list('includes')),
    "real divide_real_by_two",
    fixed = TRUE
  )
})

When running mod_w_include$format(), I get the following error (with verbose option):

Running bin/stanc PATH_TO_MODEL/bernoulli_include.stan --auto-format
Syntax error in 'PATH_TO_MODEL/bernoulli_include.stan', line 2, column 0, include error:
   -------------------------------------------------
     1:  functions {
     2:  #include divide_real_by_two.stan
         ^
     3:  }
     4:  data {
   -------------------------------------------------

Could not find include file divide_real_by_two.stan in specified include paths.

Error: Syntax error found! See the message above for more information.

Expected behavior
As can be seen above, stanc is run without the '--include-paths' argument. Weirdly, this argument is only missing when the model is precompiled, which is why the original test with an uncompiled model works perfectly fine. I get the same behavior with check_syntax. However, in contrast to format, check_syntax has the possibility to supply include_paths as an additional argument, and then it works.

CmdStanR version number
0.5.0