v1.0 stage 5: add stan_build_info() and tidy up the code around the build

[jgabry]

Submission Checklist

• Run unit tests
• Declare copyright holder and agree to license (see below)

Summary

This PR and the summary below were assisted by AI. I have reviewed all code and doc.

---

Part of #1258. This is Stage 5, the last of the feature stages: the public function that reads a build record back, plus three cleanup commits over the code the earlier stages wrote.

stan_build_info(exe_file) reads the record beside an executable and returns a stan_build_info object. Two fields are always there: record, with status and, when the record cannot be used, a reason (missing, unreadable, executable_mismatch, or unsupported_format with the format_version found); and reported_features, what the executable says about its own build, with NA kept apart from FALSE for a feature the executable did not report. With a usable record there are four more: configuration (the cpp_options, stanc_options and include_paths the build was asked for), dependencies (each file the build read, with the path it had then and whether it exists now), cmdstan (the installation's path and version, and whether the path exists), and untracked_dependencies (files the build depended on that cmdstanr cannot follow). A field that is absent means there was no record to read it from; an empty list is a recorded empty value. The result is narrower than the record on purpose, so the record's format can change underneath it. There is a print method, and $build_info() on a CmdStanModel calls the function on the model's executable. It reads the executable and record as they are on disk now, which is the point of it, so it does not go through the same check as the methods that run the executable.

The ?CmdStanModel methods tables are regrouped around the program and the executable now that $compile() is gone, and gain $variables(), which was missing. The cmdstan_model() docs for cpp_options and stanc_options now say how an entry is written and point at stan_build_info() for an example.

The second commit goes over every internal roxygen block and comment the v1.0 stages wrote, so each has a title, its fields, and wording that stands without the design doc. A few names changed with it: the record checkers are assert_record_*(), assess_build() takes expected rather than wanted, constructor_message() is build_message(), and test-model-guard.R is test-model-stale-executable.R. install_executable() moved from utils.R to build.R beside its only caller, with its tests.

The third commit gives two groups of functions files of their own. Everything that talks to stanc, from model.R and utils.R, is now R/stanc.R; the Rcpp code behind $init_model_methods() and $expose_functions(), from utils.R, is now R/expose.R. Two exe-info helpers join their only caller in build_record.R, tbb_path() moves from run.R to path.R, and cpp_opts.R is renamed cpp_options.R after the argument it handles. Every function's body is unchanged; the one non-move edit is an error in args.R that still told the user to run $compile(). The fourth commit moves the unit tests of those functions into test-stanc.R and test-build-record.R to match.

Also removes tests/testthat/testthat-problems.rds, committed by accident in #1277, and ignores testthat's problem files from now on.

Not in this PR: the development-version NEWS entries that still describe $compile(), which the pre-RC NEWS pass rewrites.

Targeted test files run locally: test-build-info, test-build-record, test-build-assess, test-build-record-compile, test-build-install, test-model-stale-executable, test-model-rebuild-rules, test-model-compile, test-model-expose-functions, test-model-methods, test-cpp-options, test-utils, test-stanc, all passing.

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):
Jonah Gabry

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/)

[jgabry]

@andrjohns just wanted to give you a heads up that this also does some file reorganization that includes moving your code to expose Stan functions and model methods into a dedicated expose.R. I think that and some other file reorganization makes the code in the repo easier to find and follow.

[codecov-commenter]

Codecov Report

❌ Patch coverage is 96.94960% with 23 lines in your changes missing coverage. Please review.
⚠️ Please upload report for BASE (v1.0@cda4315). Learn more about missing BASE report.

Files with missing lines	Patch %	Lines
R/expose.R	93.23%	14 Missing ⚠️
R/build.R	93.57%	7 Missing ⚠️
R/args.R	0.00%	1 Missing ⚠️
R/build_record.R	99.45%	1 Missing ⚠️

Additional details and impacted files

@@           Coverage Diff           @@
##             v1.0    #1278   +/-   ##
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  Coverage        ?   93.37%           
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  Files           ?       19           
  Lines           ?     7200           
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  Hits            ?     6723           
  Misses          ?      477           
  Partials        ?        0           

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