feat: replace logger with lightweight console logging + ZIP export

[Gero1999]

Issue

Closes #1210

Merges reviewed changes from:

• feat: add log-points for NCA user input changes #1221 — NCA input log-points (settings, parameters, slopes, exclusions)
• docs: document session log contents #1222 — Session log documentation (log file header, vignette, pkgdown page)

What to review

Most of the diff comes from child PRs that were already reviewed and merged into this branch. The new code unique to this PR is:

File	What's new
inst/shiny/functions/logging.R	The entire logging system (~84 lines)
inst/shiny/functions/utils.R	Removal of old setup_logger()
inst/shiny/modules/tab_nca/zip.R	session_log added to TREE_LIST$extras
inst/shiny/functions/zip-utils.R	.export_session_log() function
inst/shiny/modules/tab_nca.R	setup_logger() call
DESCRIPTION / NAMESPACE / R/imports-shiny.R	logger package removal

Everything else in the diff is either from #1221 (log-points), #1222 (documentation), or merge commits from main.

Description

Replaces the logger package with a lightweight internal logging system. Log messages are written to the R console via message() and captured in an in-memory buffer that is exported as session_log.txt in the ZIP download.

Core logging system

• New inst/shiny/functions/logging.R with log_trace, log_debug, log_info, log_success, log_warn, log_error
• In-memory buffer (get_log_buffer()) for ZIP export
• Configurable threshold via aNCA_LOG_LEVEL env var (default: INFO)
• Removed logger from Imports and Suggests, removed setup_logger() from utils.R

NCA input log-points (#1221 — already reviewed)

• Analyte, specimen, profile, method, min half-life points, flag rules, BLQ strategy, C0 imputation changes logged at INFO
• Parameter selection count per study type logged at INFO (debounced)
• Slope rule changes logged at INFO (only on user actions, not programmatic updates)
• Exclusion add/remove logged at INFO
• Initialization noise suppressed via filters_initialized guard

Session log documentation (#1222 — already reviewed)

• session_log.txt includes a header block explaining contents, threshold, and link to reference page
• vignettes/session_log.Rmd — full reference of logged events by workflow stage
• Added "Session Log Reference" to pkgdown navbar under Developer Resources
• Scope clarification added to logging.R header

ZIP export

• session_log added to TREE_LIST$extras (available with or without NCA results)
• .export_session_log() writes the buffer with header to session_log.txt

Definition of Done

• logger package fully removed (no imports, no Suggests, no require)
• All existing log_* calls work with the new system
• NCA user input changes appear in the session log
• session_log.txt exported in ZIP with explanatory header
• No log noise during initialization or settings restore

How to test

1. Run aNCA::run_app()
2. Upload data, map columns, navigate to NCA
3. Change settings (analyte, method, flag rules, etc.), add/remove slope rules and exclusions
4. Verify log messages appear in the R console
5. Export ZIP — verify session_log.txt is present with header and log entries
6. Set aNCA_LOG_LEVEL=TRACE 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

The logger package is fully removed — not just from Imports but also from Suggests and NAMESPACE. The @importFrom logger log_info in R/imports-shiny.R has been removed.

The parameter selection logging was adapted to main's matrix-based UI (the old sub-module approach via param_selector_panel_server no longer exists).

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