PregnancyIdentifier 3.1.0

Algorithm changes

Restored all 5 PPS source domains (condition_occurrence, procedure_occurrence,
observation, measurement, visit_occurrence). v3.0.0 had dropped observation
and visit_occurrence; they are now included again as a precaution even though
current PPS concepts do not map to those domains. (Just to be on the safe side.)

Replaced time-overlap summary metric with three directional date-difference
measures (PET minus algorithm): start date difference, end date difference,
and duration difference. Reported as mean/median/SD/min/Q25/Q75/max.
Added outcome-stratified date differences (same start/end/duration
differences broken down by algorithm outcome category: LB, SB, SA, AB, etc.).
Added binned date-difference distributions for episode alignment
visualisation (bins from "≤ -30 days" through "0" to "≥ 30 days"),
both overall and stratified by outcome.
Removed the time_overlap_summary metric from new output (overlap days was
confounded by episode length). Old result files with this metric are still
supported in the Shiny app.

Complete rewrite of the Shiny app: replaced legacy single-file app.R with
modular architecture using global.R, ui.R, server.R, and per-tab
modules in utils/.
Added new Alignment tab to PET comparison: interactive histogram showing
the distribution of start/end/duration date differences between matched PET
and algorithm episodes, with colour-coded bins (green = exact match,
red = large discrepancy). Supports filtering by measure and stratification
by outcome.
Added descriptive labels to PET comparison: all variable names in the
summarised result now use human-readable labels (e.g. "Start date difference
(PET - Algorithm, days)"). Legacy short labels from older result files are
automatically remapped for display.
Added backward-compatible display label remapping so the app works with both
old (pre-v3.1.0) and new result files.
Added explanatory notes to the Pregnancy Overlap tab (sequential/lag-based
check) and the Quality Check Cleanup tab (all-pairs check) explaining why
overlap counts may differ between them.
Added Overview tab with markdown methodology description for PET comparison.
Added episode and person count denominators to the precision days export.
Various UI improvements: formatted tables, interactive plotly charts, download
buttons for plots and tables.

gestational_duration_counts.csv now includes episode_count and
person_count columns per outcome category.
Added precision_days_denominators.csv to the export folder.

Updated PET comparison vignette: removed time-overlap section, added sections
for date differences, date differences by outcome, and alignment distributions.
Added extras/algorithm_improvements_v2_v3.md summarising episode-count
differences between v2 and v3.
Added extras/v2_vs_v3_episode_drop.md with detailed analysis of why
episode/person counts differ.