Use fresh to fill gaps between patchy floodplain polygons before photo selection

[NewGraphEnvironment]

Problem

The flooded VCA produces patchy floodplain polygons — gaps between modelled floodplain chunks where the algorithm can't detect lateral habitat (steep banks, narrow canyon sections, model resolution limits). These gaps don't mean the riverscape stops being interesting. A side channel, wetland, or cottonwood stand can exist in a "gap" that the model misses.

When diggs uses the raw floodplain polygon as the AOI for photo selection, these gaps can create holes in ortho coverage. The footprint filter method helps — it's generous enough to catch photos whose coverage extends across gaps — but it's not guaranteed, especially for narrow gaps between patchy floodplain chunks on smaller tributaries.

Proposed Solution (in fresh)

fresh (FWA-Referenced Spatial Hydrology, NewGraphEnvironment/sred-2025-2026#18) should provide network-aware AOI preparation that:

1. Prune isolated upstream fragments — frs_prune_isolated() drops dead-end floodplain pockets on upper tributaries (Foxy Creek, Crow Creek problem)
2. Buffer gaps between retained chunks — frs_buffer_gaps() adds buffered stream corridors between surviving floodplain polygons so the AOI covers the full riverscape, not just the modelled floodplain. This mirrors what bcfishpass does in the lateral habitat generator — buffers on all streams, side channels, and wetlands included.
3. Return a continuous AOI — the union of retained floodplain polygons + buffered gap-fill corridors, ready for diggs or drift

The network query driving this is the same frs_upstream() / frs_downstream() infrastructure fresh already needs. The buffer width could scale with stream order or channel width from bcfishpass.

Context

Discovered during diggs vignette — Neexdzii Kwah 1968 airphoto selection. Footprint filtering (258 photos) is much better than centroid filtering (40 photos) but gaps in the patchy floodplain AOI could still leave holes in ordered ortho coverage. The fix belongs in fresh, not diggs — diggs just consumes whatever AOI it's given.

Relates to NewGraphEnvironment/sred-2025-2026#18
Relates to NewGraphEnvironment/sred-2025-2026#15

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Progress update

The solution ended up splitting across packages differently than originally proposed:

Done

fresh — stream network queries replace raw SQL:

• frs_network_prune() replaces hand-written FWA_Upstream() SQL in floodplain_co.R
• frs_network() fetches streams + wetlands + lakes in one call
• frs_clip() clips waterbodies to AOI
• frs_watershed_at_measure() replaces fwapgr::fwa_watershed_at_measure()

flooded — patch operations (new):

• fl_patch_conn(valleys, stream_r) — keeps only floodplain patches connected to streams (replaces area-based pruning stopgap)
• fl_patch_rm(valleys, min_area) — removes small patches by area threshold (clean version of fragment pruning)

diggs (this branch 20-fresh-network-pruning):

• Merged duplicate scripts into area-neutral floodplain_co.R
• Swapped raw SQL for frs_network_prune()
• Renamed vignette to floodplain-select.Rmd
• Discovered bcfishpass lake/wetland habitat scoring gap (CO rearing model scores lake/wetland segments as non-habitat (rearing=0) bcfishpass#7)

Remaining

• Update floodplain_co.R to use fl_patch_conn() + fl_patch_rm() for network-aware pruning
• Update cache_data.R to use frs_watershed_at_measure() (replace fwapgr dependency)
• Update vignette pruning section to show fl_patch_conn() / fl_patch_rm() instead of area-based stopgap
• fl_valley_fill() (flooded#23) — buffer streams in gaps, union with floodplain + wetlands + lakes → continuous AOI. This is the last piece; depends on the patch functions above working well first.

Revised architecture

Step	Package	Function
Stream network	fresh	frs_network_prune()
Watershed AOI	fresh	frs_watershed_at_measure()
Wetlands/lakes	fresh	frs_network() + frs_clip()
VCA floodplain	flooded	fl_valley_confine()
Drop disconnected patches	flooded	fl_patch_conn()
Drop tiny fragments	flooded	fl_patch_rm()
Gap-fill to continuous AOI	flooded	fl_valley_fill() (future)
Photo selection	fly + diggs	fly_select() + Shiny app

[NewGraphEnvironment]

Closed via #24 (merged at 1b188c3). Raw SQL replaced with fresh, dual stream order anchor, waterbody fill, falls exclusion, 4 AOI variants output.