docs: registration-prep documentation fixes (api_overview, agent-guide page, CITATION.cff)

[kalidke]

Documentation, README, api_overview, and citation fixes from the 2026-09-05 registration-readiness review (dev/output/registration_readiness_20260905.md, items C1–C4, D6). Companion to #47 (code + CI); independent of it.

api_overview.md (root AI-parseable reference) — every item verified against the live module

• FitInfo → GaussMLEFitInfo (the former does not exist); elapsed_ns::UInt64 → elapsed_s::Float64 on all 7 info structs; stale field lists of BoxesInfo/FrameConnectInfo/DriftInfo/RenderInfo completed (n_rois, n_filtered + calibration, roi_indices + residual_correlation, scalebar_length_um); a native-info-types list added.
• Defaults corrected: DriftConfig(maxn=100), BaGoLConfig(n_iterations=4000, posterior_pixel_size=0.001) (+ se_adjust), FilterConfig criteria all default to nothing (+ z, sigma_z), IntensityFilterConfig full field list (p2_method=:mixture …), DetectFitConfig (+ datasets, pixel_size, qe, movie_fps), AnalysisConfig.checkpoint, MultiTargetConfig.verbose, MultiTargetResult.step_infos/outdir.
• Step-info table was steps-Dict residue (:filter → nothing, :detectfit → tuple); now the real types.
• save_pipeline_state(...; step_records) → step_infos (the old kwarg throws).
• data, info = load_smart_h5(path) → that function returns ONE array, so the old line silently bound two pixel values; now documents the single return and points to smart_h5_to_array for the pair.

Docs (docs/src)

• New page workflows/agent_guide.md — install_agent_guide / uninstall_agent_guide / agent_guide_status were exported and advertised in the README but on no page of the manual. get_images added to the I/O @docs.
• install.md: the "verify the install" snippet now actually runs (it referenced undefined cam/images); the docs-build recipe no longer runs Pkg.develop(path="."), which rewrote the tracked docs/Project.toml with an absolute path; registration note reworded (all deps are registered).
• composite_render.md: clip_percentile default is :auto, not 0.99.
• crosscorr.md: zero-distance pairs are kept (bin 1), not skipped; channel-B density uses B's own FOV with a mismatch warning.
• intensityfilter.md: p₂ section described only the legacy :tail estimator; the default is the threshold-free :mixture fit — concept text + table row.
• guide.md ("unregistered dependencies"), extending.md (dangling CONTRIBUTING reference), references.md (promised CITATION.bib), tutorial.md (two wording nits).

README / repo

• Requirements paragraph (Julia version, GPU, threads); ecosystem tree now lists SMLMBaGoL and SMLMClustering.
• CITATION.cff added (GitHub "Cite this repository"). Please check the author entry (name/affiliation; add an ORCID if wanted) — it is my best guess from Project.toml.

Guard

New fast test: every symbol defined in SMLMAnalysis (not re-exported) must appear in a @docs block under docs/src — the scoped check that checkdocs=:none cannot provide. It is what would have caught the four missing pages.

Local: fast tests green; full Documenter build (warnonly=false) green — see PR comment for the run outputs.

🤖 Generated with Claude Code

[kalidke]

Local verification (kitt, Julia 1.12.6):

• Pkg.test() fast tier on this branch: 439/439 (437 + the 2 assertions of the new docs-coverage test, which passes — every symbol defined in SMLMAnalysis now appears in a @docs block).
• Full julia --project=docs docs/make.jl with warnonly=false: exit 0, no new warnings (only the pre-existing upstream MicroscopePSFs.ScalarPSF docstring-replacement notice and Documenter's "skipping deployment" outside CI). The new workflows/agent_guide page renders; docs/Project.toml stayed untouched by the build.
• Every corrected default / field in api_overview.md was read from the live module (fieldnames, constructor defaults, Base.kwarg_decl, methods), not from prose.