v0.11.0: config provenance + run stamps (#40)

[NewGraphEnvironment]

Summary

Config-bundle provenance + run stamps. Pipeline outputs that shift between runs on the same DB state can now be traced back to which input changed.

• inst/extdata/configs/{bcfishpass,default}/config.yaml carry provenance: blocks with sha256 checksums for every tracked file (12 files each). External (bcfishpass) files record source URL + upstream_sha (ea3c5d8, synced 2026-04-13) + path within source repo. Generated rules.yaml records generated_from + generated_by + generator_sha. Hand-authored files record link's git sha at edit time.
• lnk_config() parses provenance, exposes cfg$provenance. print(cfg) shows count of tracked files.
• lnk_config_verify(cfg, strict) recomputes sha256 for every provenanced file, returns (file, expected, observed, drift, missing) tibble. Warns on drift; strict = TRUE errors. digest added to Suggests.
• lnk_stamp(cfg, conn, aoi, db_snapshot) returns an lnk_stamp S3 list capturing provenance + software versions + git SHAs (3-tier fallback) + DB snapshot row counts + AOI + start_time. lnk_stamp_finish(stamp, result, end_time) finalizes; format(stamp, "markdown") renders for report appendix or run-log dump.
• data-raw/compare_bcfishpass_wsg.R emits stamp markdown at the head of every WSG run, captured into data-raw/logs/*.txt via the standard stderr redirect.

Numbers

• Tests: 360 → 453 (121 new test_thats)
• Provenance: 12 files tracked per bundle, drift = 0 in shipped state
• DB snapshot: bcfishobs.observations + fwa_stream_networks_sp row counts (2 cheap queries)

Files

• R/lnk_config.R — extended (provenance parsing)
• R/lnk_config_verify.R — new
• R/lnk_stamp.R — new (lnk_stamp, lnk_stamp_finish, format.lnk_stamp, print.lnk_stamp)
• inst/extdata/configs/bcfishpass/config.yaml — provenance: block
• inst/extdata/configs/default/config.yaml — provenance: block
• data-raw/compare_bcfishpass_wsg.R — stamp emission
• tests/testthat/test-lnk_config.R — extended
• tests/testthat/test-lnk_config_verify.R — new
• tests/testthat/test-lnk_stamp.R — new
• DESCRIPTION — digest to Suggests; 0.10.0 → 0.11.0
• NEWS.md — 0.11.0 entry

Test plan

• devtools::test(): 453 PASS, 0 FAIL
• lnk_config_verify() runs clean on both bundles
• Drift detection verified via temp config + file mutation
• lnk_stamp() runs without DB; with DB; renders markdown
• /code-check round 1: 1 fragile finding fixed (.lnk_read_git_head empty-file edge)

Cross-refs

Closes #40. Supersedes the narrow report-appendix scope of #24 (markdown rendering of the run stamp covers that consumer).

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