Add progress bars for MCMC sampling using cli's C API

[Copilot]

Plan: Add Progress Bars for MCMC Sampling

• Add cli package to DESCRIPTION as an Import and LinkingTo
• Create C API implementation using cli's native C API
• Add progress bar to MCMC.c.template main sampling loop
• Add progress bar to SAN.c.template main sampling loop
• Add progress bar to CD.c.template main sampling loop
• Add progress bar to MPLE.c dyad iteration loop
• Add progress bar to MCMC.c.template Phase 1/2 adaptive algorithm loops
• Use cli's C API directly (not R callbacks)
• Show progress bars always (not conditional on verbose)
• Revert documentation changes (will be handled manually)

Summary of Changes

Implementation complete using cli's C API:

• Added LinkingTo: cli to DESCRIPTION
• Created src/ergm_progress.h using #include <cli/progress.h> and cli C functions
• Updated all C templates to use new API with ergm_progress_bar structure
• Progress bars always show (controlled by cli's CLI_SHOULD_TICK)
• Documentation changes reverted per request (will be handled manually)

Original prompt

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This section details on the original issue you should resolve

<issue_title>Add progress bars for MCMC sampling?</issue_title>
<issue_description>{cli} has a C API: https://cli.r-lib.org/reference/progress-c.html , and it should be pretty straightforward, giving the user an idea of the progress of the current MCMC run.

We already depend on {cli} indirectly.</issue_description>

Comments on the Issue (you are @copilot in this section)

@krivit Specifically, the code that would benefit from this the most would be in src/MCMC.c.template.do_not_include_directly.h, src/SAN.c.template.do_not_include_directly.h, src/CD.c.template.do_not_include_directly.h, and src/MPLE.c.

• Fixes Add progress bars for MCMC sampling? #641

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[krivit]

@copilot use cli's C API instead.

[krivit]

@copilot use progress bars regardless of verbosity.

[Copilot]

@copilot use cli's C API instead.

Done in commit 7b1122a. Now using cli's C API directly via #include <cli/progress.h> instead of calling R functions from C. The implementation uses cli's native C functions (cli_progress_bar, cli_progress_set, cli_progress_done) and checks CLI_SHOULD_TICK to respect cli's progress bar settings.

@copilot use progress bars regardless of verbosity.

Done in commit 7b1122a. Progress bars now show regardless of verbosity level. The cli C API's CLI_SHOULD_TICK macro controls whether progress bars are displayed, which respects cli's global settings and user preferences.

[krivit]

@copilot Revert verbose.R and NEWS.Rd: documentation will be handled manually.

[Copilot]

@copilot Revert verbose.R and NEWS.Rd: documentation will be handled manually.

Done in commit 1e6594e. Reverted both man-roxygen/verbose.R and inst/NEWS.Rd to their original state before any documentation changes were made.