feat: replace logger with lightweight console logging + ZIP export

[Gero1999]

Issue

Closes #1210

Description

Replaces the logger package with a lightweight internal logging system. Log messages are printed to the R console and captured in memory so they can be exported as session_log.txt in the ZIP download.

What changed:

• New file inst/shiny/functions/logging.R — drop-in replacements for log_trace, log_debug, log_info, log_success, log_warn, log_error, and log_debug_list. Supports glue-style {var} interpolation and paste-style multi-argument calls. Threshold configurable via aNCA_LOG_LEVEL env var (default: INFO).
• Removed setup_logger() and log_debug_list() from utils.R (now in logging.R).
• Removed require(logger) from app.R.
• Moved logger from Imports back to Suggests in DESCRIPTION.
• Added session_log to the ZIP export tree — the in-memory log buffer is written to session_log.txt alongside session_info.txt.

What no longer happens:

• No log files are written to the filesystem (./log directory). All output goes to the console and the in-memory buffer.

Definition of Done

• App starts without logger installed.
• Log messages appear in the R console at the configured threshold level.
• ZIP export includes session_log.txt with the session's log entries.

How to test

1. Uninstall logger (or test in a clean environment).
2. Run aNCA::run_app() — should start without errors.
3. Upload data, run NCA, and observe log messages in the R console.
4. Export results as ZIP and verify session_log.txt is included with log entries.
5. Set aNCA_LOG_LEVEL=TRACE in .Renviron and verify more verbose output.

Contributor checklist

• Code passes lintr checks
• Code passes all unit tests
• New logic covered by unit tests
• New logic is documented
• App or package changes are reflected in NEWS
• Package version is incremented
• R script works with the new implementation (if applicable)
• Settings upload works with the new implementation (if applicable)
• If any .scss change was done, run data-raw/compile_css.R

Notes to reviewer

All 48 existing log_* calls across the Shiny modules work unchanged — the new functions have the same signatures and support both glue interpolation (log_info(\"Processing {n} items\")) and paste-style (log_info(\"Processing: \", n, \" items\")).

The aNCA_LOG_LEVEL env var is still respected, same as before.

Version bump and NEWS entry still needed before merge.

[bachapman]

With this, are there any contributing guidelines for what activity should be logged and what should not be? For reference for future function/feature implementation.

[Gero1999]

@bachapman good point Bryce, probably we can include something for this. Either add a website page for the log file and then add the link somewhere in the App.

Perhaps would be also a good idea to put a help button in the Export modal message with all output explanations/links.

[Gero1999]

Or maybe is easier if we add commented lines at the top of the file to explain what is captured. Currently we are tracking this, the strategy is always to capture errors/warnings in the most data-sensitive points (mapping, NCA settings, NCA run):

Workflow Stage	What's Logged	Levels
Startup	App initialization	INFO
Data Upload	File paths, load success/failure, file errors	INFO, SUCCESS, ERROR
Settings	Settings restore/load success, load failures	SUCCESS, ERROR
Data Mapping	Mapping start, mapping warnings, mapping errors	INFO, WARN, ERROR
Data Filtering	Filter warnings	WARN
NCA Setup	Parameter selection count, PKNCA object lifecycle, units, slope edits	INFO, TRACE, SUCCESS
NCA Calculation	Calculation start, warnings (e.g. half-life issues), success, errors	INFO, WARN, SUCCESS, ERROR
Exploration Plots	Plot render, save, remove	INFO
TLG Generation	Module attachment, submitted TLG list	TRACE, DEBUG
Export	Summary stats download	INFO