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docs(cli): regenerate the CLI reference — typer 0.27 help format, new nlm and zot fetch pages
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Browse Source
This commit is contained in:
kert
2026-10-27 14:23:42 -04:00
parent bee5f57893
commit d1165cde45
98 changed files with 682 additions and 560 deletions
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11
docs/docs/cli/api-serve.md
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@@ -11,11 +11,10 @@ Usage: stack api serve [OPTIONS]
Start the stack API server.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --host TEXT Bind address. │
│ --port INTEGER Port number. │
│ --workers INTEGER Number of workers. │
│ --reload --no-reload Enable auto-reload. │
│ [default: no-reload] │
│ --help Show this message and exit. │
│ --host <str> Bind address. │
│ --port <int> Port number. │
│ --workers <int> Number of workers. │
│ --reload --no-reload Enable auto-reload. [default: no-reload] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

14
docs/docs/cli/bcda-adopt.md
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@@ -6,18 +6,18 @@ sidebar_position: 16
# `stack bcda adopt`
```
Usage: stack bcda adopt [OPTIONS] JOB_ID
Usage: stack bcda adopt [OPTIONS] {job_id}
Download a completed job this store did not start.
╭─ Arguments ──────────────────────────────────────────────────────────────────╮
│ * job_id TEXT Server job id (see `stack bcda jobs`). [required] │
│ * job_id <str> Server job id (see `stack bcda jobs`). [required] │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --preset TEXT Public sandbox entity when BCDA_CLIENT_ID is unset. │
│ [default: Large Model Entity] │
│ --type -t TEXT Resource type(s) the job holds, for the store │
│ record. │
│ --help Show this message and exit. │
│ --preset <str> Public sandbox entity when BCDA_CLIENT_ID is unset. │
│ [default: Large Model Entity] │
│ --type -t <str> Resource type(s) the job holds, for the store │
│ record. │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

6
docs/docs/cli/bcda-auth.md
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@@ -11,8 +11,8 @@ Usage: stack bcda auth [OPTIONS]
Issue a token and show attribution status.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --preset TEXT Public sandbox entity when BCDA_CLIENT_ID is unset. │
│ [default: Large Model Entity] │
│ --help Show this message and exit. │
│ --preset <str> Public sandbox entity when BCDA_CLIENT_ID is unset. │
│ [default: Large Model Entity] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

10
docs/docs/cli/bcda-cancel.md
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@@ -6,16 +6,16 @@ sidebar_position: 18
# `stack bcda cancel`
```
Usage: stack bcda cancel [OPTIONS] JOB_ID
Usage: stack bcda cancel [OPTIONS] {job_id}
Cancel an in-progress job.
╭─ Arguments ──────────────────────────────────────────────────────────────────╮
│ * job_id TEXT Server job id. [required] │
│ * job_id <str> Server job id. [required] │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --preset TEXT Public sandbox entity when BCDA_CLIENT_ID is unset. │
│ [default: Large Model Entity] │
│ --help Show this message and exit. │
│ --preset <str> Public sandbox entity when BCDA_CLIENT_ID is unset. │
│ [default: Large Model Entity] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

8
docs/docs/cli/bcda-errors.md
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@@ -6,15 +6,15 @@ sidebar_position: 20
# `stack bcda errors`
```
Usage: stack bcda errors [OPTIONS] KEY
Usage: stack bcda errors [OPTIONS] {key}
OperationOutcome issues from a job's error files (a partial export).
╭─ Arguments ──────────────────────────────────────────────────────────────────╮
│ * key TEXT Store job key. [required] │
│ * key <str> Store job key. [required] │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --limit INTEGER Issues to print. [default: 50] │
│ --help Show this message and exit. │
│ --limit <int> Issues to print. [default: 50] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

20
docs/docs/cli/bcda-export.md
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@@ -11,37 +11,37 @@ Usage: stack bcda export [OPTIONS]
Run an export through the store (blocks until downloaded).
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --preset TEXT Public sandbox entity when │
│ --preset <str> Public sandbox entity when │
│ BCDA_CLIENT_ID is unset. │
│ [default: Large Model Entity] │
│ --type -t TEXT Resource type(s); default all │
│ --type -t <str> Resource type(s); default all │
│ three. │
│ --endpoint TEXT Group/all, Group/runout or │
│ --endpoint <str> Group/all, Group/runout or │
│ Patient. │
│ [default: Group/all] │
│ --since TEXT FHIR instant │
│ --since <str> FHIR instant │
│ (2026-10-01T00:00:00+00:00) │
│ or 'auto' = the per-type │
│ watermark. │
│ --force Start even when the _since │
│ checks say block. │
│ --system-type TEXT _typeFilter System-Type │
│ --system-type <str> _typeFilter System-Type │
│ tag(s). │
│ --outcome TEXT _typeFilter outcome: partial │
│ --outcome <str> _typeFilter outcome: partial │
│ and/or complete. │
│ --service-date-from TEXT _typeFilter earliest │
│ --service-date-from <str> _typeFilter earliest │
│ service-date (YYYY[-MM[-DD]], │
│ optional gt/ge/eq prefix). │
│ --service-date-to TEXT _typeFilter latest │
│ --service-date-to <str> _typeFilter latest │
│ service-date (optional lt/le │
│ prefix). │
│ --per-type --one-job One job per type (survives │
│ sandbox sweeps). │
│ [default: per-type] │
│ --cancel-retries INTEGER Restarts after server-side │
│ --cancel-retries <int> Restarts after server-side │
│ cancellation. │
│ [default: 6] │
│ --poll-interval FLOAT Seconds between status polls. │
│ --poll-interval <float> Seconds between status polls. │
│ [default: 15.0] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯

8
docs/docs/cli/bcda-jobs.md
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@@ -11,9 +11,9 @@ Usage: stack bcda jobs [OPTIONS]
Server job history for the entity (shared on the sandbox).
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --preset TEXT Public sandbox entity when BCDA_CLIENT_ID is unset. │
│ [default: Large Model Entity] │
│ --limit INTEGER Newest N jobs. [default: 25] │
│ --help Show this message and exit. │
│ --preset <str> Public sandbox entity when BCDA_CLIENT_ID is unset. │
│ [default: Large Model Entity] │
│ --limit <int> Newest N jobs. [default: 25] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

6
docs/docs/cli/bcda-preflight.md
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@@ -11,8 +11,8 @@ Usage: stack bcda preflight [OPTIONS]
/_version, /_health and metadata — no token needed.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --preset TEXT Public sandbox entity when BCDA_CLIENT_ID is unset. │
│ [default: Large Model Entity] │
│ --help Show this message and exit. │
│ --preset <str> Public sandbox entity when BCDA_CLIENT_ID is unset. │
│ [default: Large Model Entity] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

10
docs/docs/cli/bcda-resume.md
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@@ -6,16 +6,16 @@ sidebar_position: 17
# `stack bcda resume`
```
Usage: stack bcda resume [OPTIONS] KEY
Usage: stack bcda resume [OPTIONS] {key}
Finish a store job: re-poll, download missing files, record the manifest.
╭─ Arguments ──────────────────────────────────────────────────────────────────╮
│ * key TEXT Store job key (see `stack bcda store`). [required] │
│ * key <str> Store job key (see `stack bcda store`). [required] │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --preset TEXT Public sandbox entity when BCDA_CLIENT_ID is unset. │
│ [default: Large Model Entity] │
│ --help Show this message and exit. │
│ --preset <str> Public sandbox entity when BCDA_CLIENT_ID is unset. │
│ [default: Large Model Entity] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

10
docs/docs/cli/bcda-ui.md
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@@ -11,10 +11,10 @@ Usage: stack bcda ui [OPTIONS]
Launch the BCDA manager (Streamlit; /metrics when STACK_TELEMETRY is on).
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --port INTEGER Port for the Streamlit server. │
│ [default: 8501] │
│ --headless --no-headless Do not open a browser. │
│ [default: headless] │
│ --help Show this message and exit. │
│ --port <int> Port for the Streamlit server. │
│ [default: 8501] │
│ --headless --no-headless Do not open a browser. │
│ [default: headless] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

6
docs/docs/cli/bib-attach-iom.md
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@@ -14,8 +14,8 @@ Usage: stack bib attach-iom [OPTIONS]
CMS since the last run. Safe to schedule on a timer.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --pub -p TEXT Limit to specific pub numbers. Repeat for multiple. │
│ --force Re-download even if local SHA-256 matches. │
│ --help Show this message and exit. │
│ --pub -p <str> Limit to specific pub numbers. Repeat for multiple. │
│ --force Re-download even if local SHA-256 matches. │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

8
docs/docs/cli/bib-backfill-comments.md
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@@ -21,19 +21,19 @@ Usage: stack bib backfill-comments [OPTIONS]
(#662): no API key, no cap, and mirror-only comments get created.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --docket TEXT Limit to one docket (e.g. CMS-2026-2377). Without │
│ --docket <str> Limit to one docket (e.g. CMS-2026-2377). Without │
│ it the walk covers every un-enriched stub in the │
│ store — a multi-day crawl at the reg.gov rate │
│ cap. │
│ --limit -n INTEGER Cap items processed this run. 0 = no cap │
│ --limit -n <int> Cap items processed this run. 0 = no cap │
│ (multi-day crawl). │
│ [default: 0] │
│ --sleep FLOAT Seconds between API calls. 3.7s ≈ 970/hr — just │
│ --sleep <float> Seconds between API calls. 3.7s ≈ 970/hr — just │
│ under the 1000/hr reg.gov hourly cap (the binding │
│ limit; the 50/min burst cap is looser). CDN │
│ downloads are concurrent and don't count. │
│ [default: 3.7] │
│ --log PATH Append-only progress log (survives restarts). │
│ --log <path> Append-only progress log (survives restarts). │
│ [default: /tmp/bib-backfill-comments.log] │
│ --mirror Pull from the Mirrulations S3 mirror instead of │
│ the reg.gov API — bulk speed, no rate cap, also │

18
docs/docs/cli/bib-cfr-jump.md
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@@ -6,20 +6,20 @@ sidebar_position: 46
# `stack bib cfr-jump`
```
Usage: stack bib cfr-jump [OPTIONS] [REF]
Usage: stack bib cfr-jump [OPTIONS] [ref]
Bidirectional CFR cite ↔ eCFR URL (#640); optionally place the link.
╭─ Arguments ──────────────────────────────────────────────────────────────────╮
│ ref [REF] CFR cite: "42 CFR 425.400(c)(1)(iv)" or "42 CFR Part 425". │
│ ref <str> CFR cite: "42 CFR 425.400(c)(1)(iv)" or "42 CFR Part 425". │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --url TEXT Reverse mode: print the cite for an eCFR URL. │
│ --md Print a markdown link. │
│ --place Attach the link to its bib regulation item (fr_links) │
│ so the next zotero sync carries it as a child link │
│ attachment. │
│ --label TEXT Label for the placed link. │
│ --help Show this message and exit. │
│ --url <str> Reverse mode: print the cite for an eCFR URL. │
│ --md Print a markdown link. │
│ --place Attach the link to its bib regulation item (fr_links) │
│ so the next zotero sync carries it as a child link │
│ attachment. │
│ --label <str> Label for the placed link. │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

25
docs/docs/cli/bib-code-tags.md
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@@ -28,18 +28,17 @@ Usage: stack bib code-tags [OPTIONS]
merged pass.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --collection TEXT Which collection: all | comments | │
│ rules | corpus. │
│ [default: all] │
│ --anchors-only Rules only, straight from fr_anchors │
│ text — skip pgvector entirely. │
│ --dry-run Compute the merged item→codes mapping │
│ and report what would be tagged; write │
│ nothing. │
│ --max-codes-per-item INTEGER Items with more distinct codes get │
│ family: tags only (+ hand-family │
│ codes). │
│ [default: 200] │
│ --help Show this message and exit. │
│ --collection <str> Which collection: all | comments | rules │
│ | corpus. │
│ [default: all] │
│ --anchors-only Rules only, straight from fr_anchors text │
│ — skip pgvector entirely. │
│ --dry-run Compute the merged item→codes mapping and │
│ report what would be tagged; write │
│ nothing. │
│ --max-codes-per-item <int> Items with more distinct codes get │
│ family: tags only (+ hand-family codes). │
│ [default: 200] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

6
docs/docs/cli/bib-discover-pfs-rules.md
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@@ -16,9 +16,9 @@ Usage: stack bib discover-pfs-rules [OPTIONS]
(~20 rules since 2017).
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --since TEXT [default: 2017-01-01] │
│ --until TEXT │
│ --since <str> [default: 2017-01-01] │
│ --until <str> │
│ --dry-run │
│ --help Show this message and exit. │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

10
docs/docs/cli/bib-fetch-docket-comments.md
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@@ -6,7 +6,7 @@ sidebar_position: 31
# `stack bib fetch-docket-comments`
```
Usage: stack bib fetch-docket-comments [OPTIONS] DOCKET
Usage: stack bib fetch-docket-comments [OPTIONS] {docket}
Walk one docket's comments from its stored watermark; upsert as Source items.
@@ -15,15 +15,15 @@ Usage: stack bib fetch-docket-comments [OPTIONS] DOCKET
Sealed dockets are skipped unless --force.
╭─ Arguments ──────────────────────────────────────────────────────────────────╮
│ * docket TEXT reg.gov docket id, e.g. CMS-2026-2377 [required] │
│ * docket <str> reg.gov docket id, e.g. CMS-2026-2377 [required] │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --cms-id TEXT Associate comments with a specific CMS rule │
│ --cms-id <str> Associate comments with a specific CMS rule │
│ tag. │
│ --limit -n INTEGER Stop after N comments. 0 = all. [default: 0] │
│ --limit -n <int> Stop after N comments. 0 = all. [default: 0] │
│ --attachments Also download each comment's PDF/DOCX │
│ attachments. │
│ --sleep FLOAT Seconds between API calls (rate budget). │
│ --sleep <float> Seconds between API calls (rate budget). │
│ [default: 1.3] │
│ --force Walk from page 1 even if sealed / │
│ watermarked. Never unseals. │

10
docs/docs/cli/bib-fetch-pfs-comments.md
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@@ -18,14 +18,14 @@ Usage: stack bib fetch-pfs-comments [OPTIONS]
even under `--docket`: see that option's help.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --since TEXT [default: 2017-01-01] │
│ --until TEXT │
│ --since <str> [default: 2017-01-01] │
│ --until <str> │
│ --attachments │
│ --per-docket-limit INTEGER Cap comments fetched per docket. 0 = │
│ --per-docket-limit <int> Cap comments fetched per docket. 0 = │
│ unlimited. │
│ [default: 0] │
│ --sleep FLOAT [default: 1.3] │
│ --docket TEXT Only pull this reg.gov docket (e.g. │
│ --sleep <float> [default: 1.3] │
│ --docket <str> Only pull this reg.gov docket (e.g. │
│ CMS-2026-2377). Filtered before any API │
│ call ONLY once the docket is known (a │
│ `dockets` row already exists for its CMS │

8
docs/docs/cli/bib-fr-grab.md
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@@ -14,9 +14,9 @@ Usage: stack bib fr-grab [OPTIONS]
``fr_anchor_docs`` for offline jump-link resolution.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --key TEXT Grab one rule item by bib key. │
│ --all Backfill every rule item with an FR URL. │
│ --force Re-grab even if an anchor map already exists. │
│ --help Show this message and exit. │
│ --key <str> Grab one rule item by bib key. │
│ --all Backfill every rule item with an FR URL. │
│ --force Re-grab even if an anchor map already exists. │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

20
docs/docs/cli/bib-fr-jump.md
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@@ -6,21 +6,21 @@ sidebar_position: 45
# `stack bib fr-jump`
```
Usage: stack bib fr-jump [OPTIONS] REF
Usage: stack bib fr-jump [OPTIONS] {ref}
Resolve an FR citation to its web jump link (#637); optionally place it.
╭─ Arguments ──────────────────────────────────────────────────────────────────╮
│ * ref TEXT FR reference: "91 FR 44218", "91 FR 44218 ¶3", "p-3600", │
│ or a quote. │
│ [required] │
│ * ref <str> FR reference: "91 FR 44218", "91 FR 44218 ¶3", │
│ "p-3600", or a quote. │
│ [required] │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --key TEXT Bib item key to scope resolution. │
│ --md Print a markdown link. │
│ --place Record the link in fr_links so the next zotero sync │
│ carries it as a child link attachment. │
│ --label TEXT Label for the placed link. │
│ --help Show this message and exit. │
│ --key <str> Bib item key to scope resolution. │
│ --md Print a markdown link. │
│ --place Record the link in fr_links so the next zotero sync │
│ carries it as a child link attachment. │
│ --label <str> Label for the placed link. │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

26
docs/docs/cli/bib-import-zotero.md
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@@ -21,18 +21,18 @@ Usage: stack bib import-zotero [OPTIONS]
applies.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ * --collection TEXT Zotero collection name to pull │
│ from. │
│ [required] │
│ --with-files --no-with-files Only import items that have at │
│ least one attachment file. │
│ [default: no-with-files] │
│ --only TEXT Title substring filter │
│ (case-insensitive). │
│ --tag TEXT Tag every imported item with │
│ this. Repeat for multiple. │
│ --dry-run Report what would happen without │
│ writing. │
│ --help Show this message and exit. │
│ * --collection <str> Zotero collection name to pull │
│ from. │
│ [required] │
│ --with-files --no-with-files Only import items that have at │
│ least one attachment file. │
│ [default: no-with-files] │
│ --only <str> Title substring filter │
│ (case-insensitive). │
│ --tag <str> Tag every imported item with │
│ this. Repeat for multiple. │
│ --dry-run Report what would happen │
│ without writing. │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

6
docs/docs/cli/bib-ingest-iom.md
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@@ -15,8 +15,8 @@ Usage: stack bib ingest-iom [OPTIONS]
advertises.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --pub -p TEXT Limit to specific pub numbers (e.g. 100-02). Repeat │
│ for multiple. │
│ --help Show this message and exit. │
│ --pub -p <str> Limit to specific pub numbers (e.g. 100-02). Repeat │
│ for multiple. │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

16
docs/docs/cli/bib-ingest-mail.md
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@@ -16,13 +16,13 @@ Usage: stack bib ingest-mail [OPTIONS]
tagged ``source:email`` into the appropriate Zotero collection.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --user TEXT Mailbox address to poll (must have a password in │
│ .state/mail/credentials.json). │
│ [default: cmsupdates@mail.fhirworx.io] │
│ --host TEXT [default: mail.fhirworx.io] │
│ --port INTEGER [default: 993] │
│ --folder TEXT [default: INBOX] │
│ --limit -n INTEGER [default: 0] │
│ --help Show this message and exit. │
│ --user <str> Mailbox address to poll (must have a password in │
│ .state/mail/credentials.json). │
│ [default: cmsupdates@mail.fhirworx.io] │
│ --host <str> [default: mail.fhirworx.io] │
│ --port <int> [default: 993] │
│ --folder <str> [default: INBOX] │
│ --limit -n <int> [default: 0] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

6
docs/docs/cli/bib-ingest-oig.md
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@@ -11,8 +11,8 @@ Usage: stack bib ingest-oig [OPTIONS]
Crawl OIG Compliance Program Guidance + fraud alerts indexes.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --kind -k TEXT Restrict to a subset: 'cpg' and/or 'alerts'. Repeat │
│ for multiple. │
│ --help Show this message and exit. │
│ --kind -k <str> Restrict to a subset: 'cpg' and/or 'alerts'. Repeat │
│ for multiple. │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

4
docs/docs/cli/bib-query.md
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@@ -6,12 +6,12 @@ sidebar_position: 29
# `stack bib query`
```
Usage: stack bib query [OPTIONS] TERM
Usage: stack bib query [OPTIONS] {term}
Search the bibliography store.
╭─ Arguments ──────────────────────────────────────────────────────────────────╮
│ * term TEXT Search term. [required] │
│ * term <str> Search term. [required] │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --help Show this message and exit. │

15
docs/docs/cli/bib-refresh-iom.md
View File

@@ -19,12 +19,13 @@ Usage: stack bib refresh-iom [OPTIONS]
Zotero is held (stopped) during the sync phase only.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --pub -p TEXT │
│ --file-issue --no-file-issue When watch-iom detects a │
│ futurepdf.pdf change, auto-file a │
│ Gitea issue tagged 'cms-update'. │
│ Disable for local/dev runs. │
│ [default: file-issue] │
│ --help Show this message and exit. │
│ --pub -p <str> │
│ --file-issue --no-file-issue When watch-iom detects a │
│ futurepdf.pdf change, auto-file │
│ a Gitea issue tagged │
│ 'cms-update'. Disable for │
│ local/dev runs. │
│ [default: file-issue] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

65
docs/docs/cli/bib-sync-zotero.md
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@@ -15,37 +15,38 @@ Usage: stack bib sync-zotero [OPTIONS]
duration of the sync and start it again afterward.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --tag TEXT Only sync items matching a │
│ tag. │
│ --type TEXT Only sync one item_type. │
│ --hold-zotero --no-hold Stop the 'zotero' container │
│ during sync so Zotero │
│ releases its exclusive │
│ SQLite lock; restart │
│ afterwards. │
│ [default: hold-zotero] │
│ --dedupe-collection TEXT DEPRECATED — use │
│ --merge-dupes instead, │
│ which merges rather than │
│ deletes. After the push, │
│ remove title+date │
│ duplicates from this Zotero │
│ collection (and from bib, │
│ so the next sync can't │
│ resurrect them). CMS │
│ listservs re-send identical │
│ mail with fresh │
│ Message-IDs, so duplicates │
│ otherwise accumulate — e.g. │
│ 'Cmsupdates'. │
│ --merge-dupes --no-merge-dupes After the push, merge │
│ same-URL duplicate items │
│ library-wide (union │
│ tags/collections/notes/att… │
│ keep-earliest). Supersedes │
│ --dedupe-collection, which │
│ deletes without merging. │
│ [default: no-merge-dupes] │
│ --help Show this message and exit. │
│ --tag <str> Only sync items matching a │
│ tag. │
│ --type <str> Only sync one item_type. │
│ --hold-zotero --no-hold Stop the 'zotero' │
│ container during sync so │
│ Zotero releases its │
│ exclusive SQLite lock; │
│ restart afterwards. │
│ [default: hold-zotero] │
│ --dedupe-collection <str> DEPRECATED — use │
│ --merge-dupes instead, │
│ which merges rather than │
│ deletes. After the push, │
│ remove title+date │
│ duplicates from this │
│ Zotero collection (and │
│ from bib, so the next sync │
│ can't resurrect them). CMS │
│ listservs re-send │
│ identical mail with fresh │
│ Message-IDs, so duplicates │
│ otherwise accumulate — │
│ e.g. 'Cmsupdates'. │
│ --merge-dupes --no-merge-dupes After the push, merge │
│ same-URL duplicate items │
│ library-wide (union │
│ tags/collections/notes/at… │
│ keep-earliest). Supersedes │
│ --dedupe-collection, which │
│ deletes without merging. │
│ [default: no-merge-dupes] │
│ --help Show this message and │
│ exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

4
docs/docs/cli/bib-tag.md
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@@ -6,12 +6,12 @@ sidebar_position: 28
# `stack bib tag`
```
Usage: stack bib tag [OPTIONS] [PATTERN]
Usage: stack bib tag [OPTIONS] [pattern]
List or search bibliography tags.
╭─ Arguments ──────────────────────────────────────────────────────────────────╮
│ pattern [PATTERN] Tag namespace or pattern to filter. │
│ pattern <str> Tag namespace or pattern to filter. │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --help Show this message and exit. │

16
docs/docs/cli/bls-ces.md
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@@ -14,13 +14,13 @@ Usage: stack bls ces [OPTIONS]
the per-request limits), one bib Source per series.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --series TEXT CES series id(s) to print; default all in the │
│ registry. │
│ --start INTEGER First year to pull with --write. [default: 2006] │
│ --end INTEGER Last year to pull with --write. [default: 2025] │
│ --annual Print annual means instead of months. │
│ --write Pull the registry's series, load bls.ces, cite, │
│ republish. │
│ --help Show this message and exit. │
│ --series <str> CES series id(s) to print; default all in the │
│ registry. │
│ --start <int> First year to pull with --write. [default: 2006] │
│ --end <int> Last year to pull with --write. [default: 2025] │
│ --annual Print annual means instead of months. │
│ --write Pull the registry's series, load bls.ces, cite, │
│ republish. │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

10
docs/docs/cli/bls-oews.md
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@@ -14,10 +14,10 @@ Usage: stack bls oews [OPTIONS]
cms.ingest_log. --occ prints the series.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --year INTEGER Release year(s); default 2013–. │
│ --occ TEXT SOC code(s) to print, e.g. 31-9092. │
│ --write Download, load bls.oews, cite, republish. │
│ --offline With --write: use the cached zips. │
│ --help Show this message and exit. │
│ --year <int> Release year(s); default 2013–. │
│ --occ <str> SOC code(s) to print, e.g. 31-9092. │
│ --write Download, load bls.oews, cite, republish. │
│ --offline With --write: use the cached zips. │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

10
docs/docs/cli/comments-extract-ocr.md
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@@ -18,10 +18,10 @@ Usage: stack comments extract-ocr [OPTIONS]
uv run --with rapidocr-onnxruntime stack comments extract-ocr
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --root PATH Comments root dir. [default: .state/comments] │
│ --docket TEXT Limit to one docket (e.g. CMS-2023-0121). │
│ --limit INTEGER Cap comment dirs processed this run. 0 = no cap. │
│ [default: 0] │
│ --help Show this message and exit. │
│ --root <path> Comments root dir. [default: .state/comments] │
│ --docket <str> Limit to one docket (e.g. CMS-2023-0121). │
│ --limit <int> Cap comment dirs processed this run. 0 = no cap. │
│ [default: 0] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

43
docs/docs/cli/comments-extract.md
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@@ -11,27 +11,26 @@ Usage: stack comments extract [OPTIONS]
Walk comment dirs and write combined.md (PDF/DOCX → text).
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --root PATH Comments root dir. │
│ [default: .state/comments] │
│ --docket TEXT Limit to one docket (e.g. │
│ CMS-2023-0121). │
│ --limit INTEGER Cap dirs processed this run. 0 = no │
│ cap. │
│ [default: 0] │
│ --workers INTEGER Concurrent extraction threads. │
│ [default: 8] │
│ --force Re-extract dirs that already have │
│ combined.md. │
│ --bib --no-bib Look up inline body from bib.sqlite │
│ items.abstract. │
│ [default: bib] │
│ --attach --no-attach Attach combined.md back to its bib │
│ item (so it flows to Zotero via `bib │
│ sync`). Implies --bib; no-op when │
│ --no-bib. │
│ [default: attach] │
│ --reattach Also attach combined.md notes for dirs │
│ that were already current (repair). │
│ --help Show this message and exit. │
│ --root <path> Comments root dir. │
│ [default: .state/comments] │
│ --docket <str> Limit to one docket (e.g. │
│ CMS-2023-0121). │
│ --limit <int> Cap dirs processed this run. 0 = no │
│ cap. │
│ [default: 0] │
│ --workers <int> Concurrent extraction threads. │
│ [default: 8] │
│ --force Re-extract dirs that already have │
│ combined.md. │
│ --bib --no-bib Look up inline body from bib.sqlite │
│ items.abstract. │
│ [default: bib] │
│ --attach --no-attach Attach combined.md back to its bib item │
│ (so it flows to Zotero via `bib sync`). │
│ Implies --bib; no-op when --no-bib. │
│ [default: attach] │
│ --reattach Also attach combined.md notes for dirs │
│ that were already current (repair). │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

8
docs/docs/cli/comments-seal.md
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@@ -6,15 +6,15 @@ sidebar_position: 56
# `stack comments seal`
```
Usage: stack comments seal [OPTIONS] DOCKET
Usage: stack comments seal [OPTIONS] {docket}
Mark a docket complete: every stage skips it until unsealed or --force.
╭─ Arguments ──────────────────────────────────────────────────────────────────╮
│ * docket TEXT reg.gov docket id [required] │
│ * docket <str> reg.gov docket id [required] │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --reason TEXT [default: manual] │
│ --help Show this message and exit. │
│ --reason <str> [default: manual] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

4
docs/docs/cli/comments-stats.md
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@@ -11,7 +11,7 @@ Usage: stack comments stats [OPTIONS]
Rebuild the index and print per-status counts.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --root PATH Comments root dir. [default: .state/comments] │
│ --help Show this message and exit. │
│ --root <path> Comments root dir. [default: .state/comments] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

4
docs/docs/cli/comments-unseal.md
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@@ -6,12 +6,12 @@ sidebar_position: 57
# `stack comments unseal`
```
Usage: stack comments unseal [OPTIONS] DOCKET
Usage: stack comments unseal [OPTIONS] {docket}
Reopen a sealed docket.
╭─ Arguments ──────────────────────────────────────────────────────────────────╮
│ * docket TEXT reg.gov docket id [required] │
│ * docket <str> reg.gov docket id [required] │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --help Show this message and exit. │

4
docs/docs/cli/db-inspect.md
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@@ -6,12 +6,12 @@ sidebar_position: 75
# `stack db inspect`
```
Usage: stack db inspect [OPTIONS] [TABLE]
Usage: stack db inspect [OPTIONS] [table]
Inspect DuckDB table schema and stats.
╭─ Arguments ──────────────────────────────────────────────────────────────────╮
│ table [TABLE] Table name (schema.table). │
│ table <str> Table name (schema.table). │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --help Show this message and exit. │

6
docs/docs/cli/docs-serve.md
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@@ -11,8 +11,8 @@ Usage: stack docs serve [OPTIONS]
Serve documentation locally with hot reload.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --port INTEGER Port to serve on. [default: 3000] │
│ --skip-generate Skip content generation. │
│ --help Show this message and exit. │
│ --port <int> Port to serve on. [default: 3000] │
│ --skip-generate Skip content generation. │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

14
docs/docs/cli/lake-deploy.md
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@@ -11,12 +11,12 @@ Usage: stack lake deploy [OPTIONS]
Create schemas and tables from SQLTable models.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --target TEXT Target: iceberg (nessie/polaris) or databricks. │
│ [default: iceberg] │
│ --catalog-type TEXT Catalog type: nessie or polaris. │
│ [default: nessie] │
│ --schema TEXT Only deploy these schemas. │
│ --dry-run Report without creating. │
│ --help Show this message and exit. │
│ --target <str> Target: iceberg (nessie/polaris) or databricks. │
│ [default: iceberg] │
│ --catalog-type <str> Catalog type: nessie or polaris. │
│ [default: nessie] │
│ --schema <str> Only deploy these schemas. │
│ --dry-run Report without creating. │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

11
docs/docs/cli/lake-load.md
View File

@@ -11,10 +11,11 @@ Usage: stack lake load [OPTIONS]
Populate Iceberg tables with data from DuckDB.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --catalog-type TEXT Catalog type: nessie or polaris. │
│ [default: nessie] │
│ --schema TEXT Only load these schemas. │
│ --mode TEXT Write mode: append or replace. [default: append] │
│ --help Show this message and exit. │
│ --catalog-type <str> Catalog type: nessie or polaris. │
│ [default: nessie] │
│ --schema <str> Only load these schemas. │
│ --mode <str> Write mode: append or replace. │
│ [default: append] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

4
docs/docs/cli/lake-parity.md
View File

@@ -11,7 +11,7 @@ Usage: stack lake parity [OPTIONS]
Compare pipeline outputs between DuckDB and Databricks.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --schema TEXT Only check these schemas. │
│ --help Show this message and exit. │
│ --schema <str> Only check these schemas. │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

8
docs/docs/cli/lake-validate.md
View File

@@ -11,9 +11,9 @@ Usage: stack lake validate [OPTIONS]
Validate Iceberg tables match SQLTable model definitions.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --catalog-type TEXT Catalog type: nessie or polaris. │
│ [default: nessie] │
│ --schema TEXT Only validate these schemas. │
│ --help Show this message and exit. │
│ --catalog-type <str> Catalog type: nessie or polaris. │
│ [default: nessie] │
│ --schema <str> Only validate these schemas. │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

12
docs/docs/cli/llm-eval-tags.md
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@@ -15,17 +15,17 @@ Usage: stack llm eval-tags [OPTIONS]
re-tags each golden comment now. Exit 1 when the gate fails.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --golden TEXT Golden YAML (comment ids with expected │
│ --golden <str> Golden YAML (comment ids with expected │
│ themes). │
│ [default: tests/llm/golden_themes.yaml] │
│ --live Re-tag through the model instead of scoring │
│ what is stored on the items. │
│ --limit INTEGER Score only the first N golden entries. │
│ --limit <int> Score only the first N golden entries. │
│ [default: 0] │
│ --top INTEGER [default: 8] │
│ --max-tags INTEGER [default: 3] │
│ --min-confidence FLOAT [default: 0.6] │
│ --dump TEXT With --live: write every comment's │
│ --top <int> [default: 8] │
│ --max-tags <int> [default: 3] │
│ --min-confidence <float> [default: 0.6] │
│ --dump <str> With --live: write every comment's │
│ shortlist, verdicts and confidences to this │
│ JSON file. │
│ --help Show this message and exit. │

23
docs/docs/cli/llm-index.md
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@@ -15,17 +15,16 @@ Usage: stack llm index [OPTIONS]
corpus = every non-comment bib item incl. Zotero-only storage PDFs.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --collection TEXT Which collection: comments | rules | │
│ corpus | all. │
│ [default: comments] │
│ --docket TEXT Limit comments to one docket id. │
│ --key TEXT Limit rules/corpus to these item │
│ keys. │
│ --force --no-force Re-embed even when unchanged. │
│ [default: no-force] │
│ --limit INTEGER Stop after N docs per collection (0 = │
│ all). │
│ [default: 0] │
│ --help Show this message and exit. │
│ --collection <str> Which collection: comments | rules | │
│ corpus | all. │
│ [default: comments] │
│ --docket <str> Limit comments to one docket id. │
│ --key <str> Limit rules/corpus to these item keys. │
│ --force --no-force Re-embed even when unchanged. │
│ [default: no-force] │
│ --limit <int> Stop after N docs per collection (0 = │
│ all). │
│ [default: 0] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

12
docs/docs/cli/llm-restamp.md
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@@ -21,11 +21,11 @@ Usage: stack llm restamp [OPTIONS]
under `--dry-run`.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --collection TEXT Which collection: comments | rules | corpus | │
│ all. │
│ [default: comments] │
│ --batch INTEGER Rows per transaction. [default: 2000] │
│ --dry-run Scan and report without writing. │
│ --help Show this message and exit. │
│ --collection <str> Which collection: comments | rules | corpus | │
│ all. │
│ [default: comments] │
│ --batch <int> Rows per transaction. [default: 2000] │
│ --dry-run Scan and report without writing. │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

6
docs/docs/cli/llm-serve.md
View File

@@ -11,8 +11,8 @@ Usage: stack llm serve [OPTIONS]
Serve the SSO-guarded chat UI (llm.api:app).
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --host TEXT Bind address. [default: 127.0.0.1] │
│ --port INTEGER Port. [default: 8000] │
│ --help Show this message and exit. │
│ --host <str> Bind address. [default: 127.0.0.1] │
│ --port <int> Port. [default: 8000] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

10
docs/docs/cli/llm-stamp-themes.md
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@@ -15,12 +15,12 @@ Usage: stack llm stamp-themes [OPTIONS]
them.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --collection TEXT comments | rules | corpus. [default: corpus] │
│ --doctype TEXT Only chunks of this doctype ('' = every chunk). │
│ --collection <str> comments | rules | corpus. [default: corpus] │
│ --doctype <str> Only chunks of this doctype ('' = every chunk). │
│ [default: manual] │
│ --key TEXT Only this item key. │
│ --top INTEGER Themes kept per chunk. [default: 2] │
│ --min-score FLOAT Cosine similarity a theme must reach. │
│ --key <str> Only this item key. │
│ --top <int> Themes kept per chunk. [default: 2] │
│ --min-score <float> Cosine similarity a theme must reach. │
│ [default: 0.6] │
│ --force Re-stamp chunks already on the current │
│ vocabulary version. │

10
docs/docs/cli/llm-tag.md
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@@ -15,21 +15,21 @@ Usage: stack llm tag [OPTIONS]
skipped unless --force.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ * --docket TEXT regulations.gov docket id, e.g. │
│ * --docket <str> regulations.gov docket id, e.g. │
│ CMS-2026-2377. │
│ [required] │
│ --limit INTEGER Stop after N comments (newest first; 0 = │
│ --limit <int> Stop after N comments (newest first; 0 = │
│ all). │
│ [default: 0] │
│ --force Re-tag comments whose stored state is │
│ current. │
│ --dry-run Compute and print, write nothing. │
│ --top INTEGER Themes shortlisted per comment before │
│ --top <int> Themes shortlisted per comment before │
│ judging. │
│ [default: 8] │
│ --max-tags INTEGER Most themes written per comment. │
│ --max-tags <int> Most themes written per comment. │
│ [default: 3] │
│ --min-confidence FLOAT Shortlist similarity below which a │
│ --min-confidence <float> Shortlist similarity below which a │
│ judged yes is not written. │
│ [default: 0.0] │
│ --verbose Print every comment's tags. │

8
docs/docs/cli/llm-vocab.md
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@@ -13,9 +13,9 @@ Usage: stack llm vocab [OPTIONS]
it was seeded from.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --path TEXT A vocabulary file to validate instead of the packaged │
│ one. │
│ --slug TEXT Show one theme in full. │
│ --help Show this message and exit. │
│ --path <str> A vocabulary file to validate instead of the packaged │
│ one. │
│ --slug <str> Show one theme in full. │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

12
docs/docs/cli/load-bcda.md
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@@ -16,11 +16,11 @@ Usage: stack load bcda [OPTIONS]
resource type under the BCDA store (a v3 pull is three jobs).
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --ndjson-dir PATH Directory containing FHIR ndjson files. │
│ --database TEXT DuckDB database path (default: config). │
│ --skip-flatten Skip flattening, load existing Parquet. │
│ --run-pipeline Also run the bcda connector pipeline into │
│ input_layer.* │
│ --help Show this message and exit. │
│ --ndjson-dir <path> Directory containing FHIR ndjson files. │
│ --database <str> DuckDB database path (default: config). │
│ --skip-flatten Skip flattening, load existing Parquet. │
│ --run-pipeline Also run the bcda connector pipeline into │
│ input_layer.* │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

8
docs/docs/cli/load-cclf.md
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@@ -15,9 +15,9 @@ Usage: stack load cclf [OPTIONS]
pipeline to produce ``input_layer`` tables.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ * --path PATH Directory containing CCLF files. [required] │
│ --database TEXT DuckDB database path (default: config). │
│ --no-pipeline Load raw tables only, skip CCLF pipeline. │
│ --help Show this message and exit. │
│ * --path <path> Directory containing CCLF files. [required] │
│ --database <str> DuckDB database path (default: config). │
│ --no-pipeline Load raw tables only, skip CCLF pipeline. │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

20
docs/docs/cli/load-cms.md
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@@ -17,14 +17,16 @@ Usage: stack load cms [OPTIONS]
claims or ``cms.aco_participant_tin`` know it.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --table -t TEXT cms.<table> (default: the institutional │
│ universe). │
│ --database TEXT DuckDB database path (default: config). │
│ --refresh Re-download even if the CSV is on disk. │
│ --derive --no-derive Rebuild institutional_provider / │
│ ccn_crosswalk / provider_tin_observed / │
│ ccn_tin. │
│ [default: derive] │
│ --help Show this message and exit. │
│ --table -t <str> cms.<table> (default: the │
│ institutional universe). │
│ --database <str> DuckDB database path (default: │
│ config). │
│ --refresh Re-download even if the CSV is on │
│ disk. │
│ --derive --no-derive Rebuild institutional_provider / │
│ ccn_crosswalk / provider_tin_observed │
│ / ccn_tin. │
│ [default: derive] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

10
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@@ -11,10 +11,10 @@ Usage: stack load seed [OPTIONS]
Load seed/reference data (CSV, Excel, Parquet) into DuckDB.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --seed-dir PATH Directory containing seed files. │
│ --database TEXT DuckDB database path (default: config). │
│ --schema TEXT Target DuckDB schema for seed tables. │
│ [default: reference_data] │
│ --help Show this message and exit. │
│ --seed-dir <path> Directory containing seed files. │
│ --database <str> DuckDB database path (default: config). │
│ --schema <str> Target DuckDB schema for seed tables. │
│ [default: reference_data] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

2
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@@ -1,6 +1,6 @@
---
title: stack mail attach-smarthost
sidebar_position: 122
sidebar_position: 123
---
# `stack mail attach-smarthost`

2
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@@ -1,6 +1,6 @@
---
title: stack mail dkim-export
sidebar_position: 121
sidebar_position: 122
---
# `stack mail dkim-export`

2
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@@ -1,6 +1,6 @@
---
title: stack mail dns
sidebar_position: 120
sidebar_position: 121
---
# `stack mail dns`

2
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@@ -1,6 +1,6 @@
---
title: stack mail down
sidebar_position: 118
sidebar_position: 119
---
# `stack mail down`

8
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@@ -1,6 +1,6 @@
---
title: stack mail provision
sidebar_position: 116
sidebar_position: 117
---
# `stack mail provision`
@@ -11,8 +11,8 @@ Usage: stack mail provision [OPTIONS]
End-to-end idempotent: up → wait → DNS → DKIM → smarthost → git env.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --region TEXT DO region slug (one your ISP can reach). │
│ [default: nyc3] │
│ --help Show this message and exit. │
│ --region <str> DO region slug (one your ISP can reach). │
│ [default: nyc3] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

8
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@@ -1,18 +1,18 @@
---
title: stack mail rotate-creds
sidebar_position: 123
sidebar_position: 124
---
# `stack mail rotate-creds`
```
Usage: stack mail rotate-creds [OPTIONS] USER
Usage: stack mail rotate-creds [OPTIONS] {user}
Mint a new password for *user*@fhirworx.io and push to droplet.
╭─ Arguments ──────────────────────────────────────────────────────────────────╮
│ * user TEXT Mailbox to rotate (e.g. git, postmaster, cmsupdates). │
│ [required] │
│ * user <str> Mailbox to rotate (e.g. git, postmaster, cmsupdates). │
│ [required] │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --help Show this message and exit. │

2
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@@ -1,6 +1,6 @@
---
title: stack mail seed-mailboxes
sidebar_position: 124
sidebar_position: 125
---
# `stack mail seed-mailboxes`

2
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@@ -1,6 +1,6 @@
---
title: stack mail status
sidebar_position: 119
sidebar_position: 120
---
# `stack mail status`

6
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@@ -1,6 +1,6 @@
---
title: stack mail up
sidebar_position: 117
sidebar_position: 118
---
# `stack mail up`
@@ -11,7 +11,7 @@ Usage: stack mail up [OPTIONS]
Adopt-or-create the mail droplet. Idempotent.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --region TEXT DO region slug. [default: nyc3] │
│ --help Show this message and exit. │
│ --region <str> DO region slug. [default: nyc3] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

2
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@@ -1,6 +1,6 @@
---
title: stack mail wire-git
sidebar_position: 125
sidebar_position: 126
---
# `stack mail wire-git`

2
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@@ -1,6 +1,6 @@
---
title: stack mail
sidebar_position: 115
sidebar_position: 116
---
# `stack mail`

18
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@@ -0,0 +1,18 @@
---
title: stack nlm fetch
sidebar_position: 129
---
# `stack nlm fetch`
```
Usage: stack nlm fetch [OPTIONS]
Download the current file of every (or each named) release stream.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --stream <str> Only these streams. │
│ --dest <path> Root directory (default nlm.dir). │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

17
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@@ -0,0 +1,17 @@
---
title: stack nlm releases
sidebar_position: 128
---
# `stack nlm releases`
```
Usage: stack nlm releases [OPTIONS]
List the current file of every release stream.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --stream <str> Only these streams. │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

24
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@@ -0,0 +1,24 @@
---
title: stack nlm vsac
sidebar_position: 130
---
# `stack nlm vsac`
```
Usage: stack nlm vsac [OPTIONS]
Save every VSAC value-set definition, then expand each one.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --dest <path> Root directory (default │
│ nlm.dir). │
│ --definitions-only │
│ --workers <int range> [1<=x<=16] [default: 4] │
│ --limit <int> Expand at most N (0 = │
│ all). │
│ [default: 0] │
│ --help Show this message and │
│ exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

21
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@@ -0,0 +1,21 @@
---
title: stack nlm
sidebar_position: 127
---
# `stack nlm`
```
Usage: stack nlm [OPTIONS] COMMAND [ARGS]...
NLM terminology releases and VSAC value sets.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Commands ───────────────────────────────────────────────────────────────────╮
│ releases List the current file of every release stream. │
│ fetch Download the current file of every (or each named) release stream. │
│ vsac Save every VSAC value-set definition, then expand each one. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

7
docs/docs/cli/perf-show.md
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@@ -11,9 +11,8 @@ Usage: stack perf show [OPTIONS]
Pretty-print spans from the local JSONL trace file.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --path TEXT Path to JSONL span file. │
│ [default: traces/spans.jsonl] │
│ --last INTEGER Show last N spans. [default: 20] │
│ --help Show this message and exit. │
│ --path <str> Path to JSONL span file. [default: traces/spans.jsonl] │
│ --last <int> Show last N spans. [default: 20] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

8
docs/docs/cli/pfs-cpt-ingest.md
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@@ -13,9 +13,9 @@ Usage: stack pfs cpt-ingest [OPTIONS]
2026-09-09-cpt-canonical-schema-design.md §3).
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --edition INTEGER CPT edition year to ingest (repeatable). │
│ --all Every CPT EPUB edition found in bib (source:ama). │
│ --dry-run Parse and report counts; write nothing. │
│ --help Show this message and exit. │
│ --edition <int> CPT edition year to ingest (repeatable). │
│ --all Every CPT EPUB edition found in bib (source:ama). │
│ --dry-run Parse and report counts; write nothing. │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

18
docs/docs/cli/pfs-elements.md
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@@ -11,14 +11,14 @@ Usage: stack pfs elements [OPTIONS]
Extract typed elements for codes into pfs.code_element (+ review queue).
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --code TEXT HCPCS/CPT code (repeatable). │
│ --family TEXT Expand a registered family (CCM, APCM, …); │
│ repeatable. │
│ --all-payable Every A/R/T code in the newest RVU year, one │
│ inverted pass over fr_anchors. │
│ --no-llm Skip the local-model classifier (unknown lines go │
│ to review). │
│ --dry-run Extract and report; write nothing. │
│ --help Show this message and exit. │
│ --code <str> HCPCS/CPT code (repeatable). │
│ --family <str> Expand a registered family (CCM, APCM, …); │
│ repeatable. │
│ --all-payable Every A/R/T code in the newest RVU year, one │
│ inverted pass over fr_anchors. │
│ --no-llm Skip the local-model classifier (unknown lines │
│ go to review). │
│ --dry-run Extract and report; write nothing. │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

25
docs/docs/cli/pfs-exposure.md
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@@ -18,18 +18,17 @@ Usage: stack pfs exposure [OPTIONS]
calendar); --code/--family only filter what is printed.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --code TEXT Filter to a code; repeatable. │
│ --family TEXT Filter to a family key (CCM, APCM, …); │
│ repeatable. │
│ --controls INTEGER With one --code and --year: list up to N │
│ never-treated control codes (same status + RVU │
│ band, no exposure within --window years). │
│ [default: 0] │
│ --year INTEGER The exposure year --controls refers to. │
│ [default: 0] │
│ --window INTEGER ±years a control must be quiet for. [default: 2] │
│ --write Rebuild the whole calendar into pfs.code_exposure │
│ and republish. │
│ --help Show this message and exit. │
│ --code <str> Filter to a code; repeatable. │
│ --family <str> Filter to a family key (CCM, APCM, …); repeatable. │
│ --controls <int> With one --code and --year: list up to N │
│ never-treated control codes (same status + RVU │
│ band, no exposure within --window years). │
│ [default: 0] │
│ --year <int> The exposure year --controls refers to. │
│ [default: 0] │
│ --window <int> ±years a control must be quiet for. [default: 2] │
│ --write Rebuild the whole calendar into pfs.code_exposure │
│ and republish. │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

4
docs/docs/cli/pfs-guidance.md
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@@ -13,8 +13,8 @@ Usage: stack pfs guidance [OPTIONS]
CPT manual cite, with FR provenance.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --family TEXT Family key (CCM, APCM, …); repeatable. │
│ --family <str> Family key (CCM, APCM, …); repeatable. │
│ --write │
│ --help Show this message and exit. │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

16
docs/docs/cli/pfs-lineage.md
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@@ -14,13 +14,13 @@ Usage: stack pfs lineage [OPTIONS]
fr_anchors instead of one query per code.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --code TEXT │
│ --all-payable Every A/R/T code in the newest RVU year, one │
│ inverted pass over fr_anchors. │
│ --limit INTEGER Only the first N target codes (sorted) — for │
│ smoke runs with --all-payable. │
│ [default: 0] │
│ --write Persist to pfs.code_event and republish. │
│ --help Show this message and exit. │
│ --code <str> │
│ --all-payable Every A/R/T code in the newest RVU year, one │
│ inverted pass over fr_anchors. │
│ --limit <int> Only the first N target codes (sorted) — for │
│ smoke runs with --all-payable. │
│ [default: 0] │
│ --write Persist to pfs.code_event and republish. │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

18
docs/docs/cli/pfs-reaction.md
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@@ -16,15 +16,15 @@ Usage: stack pfs reaction [OPTIONS]
persisting the result.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --family TEXT Family key (CCM, APCM, …); repeatable. │
│ --code TEXT A single code as its own pseudo-family, │
│ keyed by the code; repeatable. │
│ --stance-sample INTEGER Classify the newest N commenters per docket │
│ into support/oppose/modify/unclear via the │
│ self-hosted classifier (0 = skip; no stance │
│ sample means no LLM call at all). │
│ [default: 0] │
│ --family <str> Family key (CCM, APCM, …); repeatable. │
│ --code <str> A single code as its own pseudo-family, keyed │
│ by the code; repeatable. │
│ --stance-sample <int> Classify the newest N commenters per docket │
│ into support/oppose/modify/unclear via the │
│ self-hosted classifier (0 = skip; no stance │
│ sample means no LLM call at all). │
│ [default: 0] │
│ --write │
│ --help Show this message and exit. │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

4
docs/docs/cli/pfs-review.md
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@@ -11,7 +11,7 @@ Usage: stack pfs review [OPTIONS]
Element lines the classifier could not place.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --code TEXT │
│ --help Show this message and exit. │
│ --code <str> │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

18
docs/docs/cli/pfs-utilization.md
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@@ -18,14 +18,14 @@ Usage: stack pfs utilization [OPTIONS]
republishes the replica; --code prints series from the replica.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --year INTEGER Calendar year(s) to ingest with --write; default │
│ all 2013–. │
│ --code TEXT Print the per-year series for these codes │
│ (repeatable). │
│ --write Fetch from data.cms.gov, load pfs.utilization, │
│ cite, republish. │
│ --offline With --write: load from the cached JSON instead of │
│ the API. │
│ --help Show this message and exit. │
│ --year <int> Calendar year(s) to ingest with --write; default all │
│ 2013–. │
│ --code <str> Print the per-year series for these codes │
│ (repeatable). │
│ --write Fetch from data.cms.gov, load pfs.utilization, cite, │
│ republish. │
│ --offline With --write: load from the cached JSON instead of │
│ the API. │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

52
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@@ -1,41 +1,41 @@
---
title: stack prisma eligible
sidebar_position: 109
sidebar_position: 110
---
# `stack prisma eligible`
```
Usage: stack prisma eligible [OPTIONS] NAME
Usage: stack prisma eligible [OPTIONS] {name}
Stage 3 — LLM-driven full-text eligibility pass.
╭─ Arguments ──────────────────────────────────────────────────────────────────╮
│ * name TEXT Project slug. [required] │
│ * name <str> Project slug. [required] │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --limit -n INTEGER [default: 0] │
│ --max-chars INTEGER Cap per-item markdown (full text) │
│ at N chars so bounded-context local │
│ models keep the criteria in window. │
│ 0 = no cap. │
│ [default: 0] │
│ --db PATH [default: │
│ data/zotero/data/zotero.sqlite] │
│ --storage PATH [default: data/zotero/data/storage] │
│ --hold --no-hold [default: hold] │
│ --hosts TEXT Comma-separated Ollama base URLs — │
│ fleet mode (#655): parallel │
│ eligibility via native /api/chat │
│ with per-request num_ctx; bypasses │
│ PRISMA_LLM_* env config. │
│ --fleet-model TEXT Model name on every fleet host. │
│ [default: qwen2.5:14b] │
│ --num-ctx INTEGER Context window per fleet request. │
│ [default: 8192] │
│ --per-host INTEGER Max in-flight requests per fleet │
│ host. │
│ [default: 1] │
│ --help Show this message and exit. │
│ --limit -n <int> [default: 0] │
│ --max-chars <int> Cap per-item markdown (full text) at │
│ N chars so bounded-context local │
│ models keep the criteria in window. │
│ 0 = no cap. │
│ [default: 0] │
│ --db <path> [default: │
│ data/zotero/data/zotero.sqlite] │
│ --storage <path> [default: data/zotero/data/storage] │
│ --hold --no-hold [default: hold] │
│ --hosts <str> Comma-separated Ollama base URLs — │
│ fleet mode (#655): parallel │
│ eligibility via native /api/chat │
│ with per-request num_ctx; bypasses │
│ PRISMA_LLM_* env config. │
│ --fleet-model <str> Model name on every fleet host. │
│ [default: qwen2.5:14b] │
│ --num-ctx <int> Context window per fleet request. │
│ [default: 8192] │
│ --per-host <int> Max in-flight requests per fleet │
│ host. │
│ [default: 1] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

14
docs/docs/cli/prisma-export.md
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@@ -1,23 +1,23 @@
---
title: stack prisma export
sidebar_position: 106
sidebar_position: 107
---
# `stack prisma export`
```
Usage: stack prisma export [OPTIONS] ZOT_ID
Usage: stack prisma export [OPTIONS] {zot_id}
Dump one Zotero item as the LLM-ready markdown snapshot.
╭─ Arguments ──────────────────────────────────────────────────────────────────╮
│ * zot_id INTEGER Zotero itemID to export. [required] │
│ * zot_id <int> Zotero itemID to export. [required] │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --fulltext │
│ --db PATH [default: data/zotero/data/zotero.sqlite] │
│ --storage PATH [default: data/zotero/data/storage] │
│ --hold --no-hold [default: hold] │
│ --help Show this message and exit. │
│ --db <path> [default: data/zotero/data/zotero.sqlite] │
│ --storage <path> [default: data/zotero/data/storage] │
│ --hold --no-hold [default: hold] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

42
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@@ -1,36 +1,36 @@
---
title: stack prisma extract
sidebar_position: 110
sidebar_position: 111
---
# `stack prisma extract`
```
Usage: stack prisma extract [OPTIONS] NAME
Usage: stack prisma extract [OPTIONS] {name}
Stage 3+ — structured data extraction on included studies.
╭─ Arguments ──────────────────────────────────────────────────────────────────╮
│ * name TEXT Project slug. [required] │
│ * name <str> Project slug. [required] │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --limit -n INTEGER [default: 0] │
│ --db PATH [default: │
│ data/zotero/data/zotero.sqlite] │
│ --storage PATH [default: data/zotero/data/storage] │
│ --hold --no-hold [default: hold] │
│ --hosts TEXT Comma-separated Ollama base URLs — │
│ fleet mode (#655): parallel │
│ extraction via native /api/chat │
│ with per-request num_ctx; bypasses │
│ PRISMA_LLM_* env config. │
│ --fleet-model TEXT Model name on every fleet host. │
│ [default: qwen2.5:14b] │
│ --num-ctx INTEGER Context window per fleet request. │
│ [default: 8192] │
│ --per-host INTEGER Max in-flight requests per fleet │
│ host. │
│ [default: 1] │
│ --help Show this message and exit. │
│ --limit -n <int> [default: 0] │
│ --db <path> [default: │
│ data/zotero/data/zotero.sqlite] │
│ --storage <path> [default: data/zotero/data/storage] │
│ --hold --no-hold [default: hold] │
│ --hosts <str> Comma-separated Ollama base URLs — │
│ fleet mode (#655): parallel │
│ extraction via native /api/chat with │
│ per-request num_ctx; bypasses │
│ PRISMA_LLM_* env config. │
│ --fleet-model <str> Model name on every fleet host. │
│ [default: qwen2.5:14b] │
│ --num-ctx <int> Context window per fleet request. │
│ [default: 8192] │
│ --per-host <int> Max in-flight requests per fleet │
│ host. │
│ [default: 1] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

47
docs/docs/cli/prisma-fetch.md
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@@ -1,12 +1,12 @@
---
title: stack prisma fetch
sidebar_position: 112
sidebar_position: 113
---
# `stack prisma fetch`
```
Usage: stack prisma fetch [OPTIONS] NAME
Usage: stack prisma fetch [OPTIONS] {name}
Fetch PDFs for every non-excluded item lacking an attachment.
@@ -21,29 +21,28 @@ Usage: stack prisma fetch [OPTIONS] NAME
the duration of the fetch and closes it on exit. No sudo required.
╭─ Arguments ──────────────────────────────────────────────────────────────────╮
│ * name TEXT Project slug. [required] │
│ * name <str> Project slug. [required] │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --limit -n INTEGER [default: 0] │
│ --workers -w INTEGER Concurrent fetch workers (fallback │
│ tier stays serialized). │
│ [default: 8] │
│ --db PATH [default: │
│ data/zotero/data/zotero.sqlite] │
│ --storage PATH [default: data/zotero/data/storage] │
│ --scratch PATH [default: .state/prisma-fetch] │
│ --proxy TEXT Override PRISMA_FETCH_PROXY (else │
│ env). │
│ --vpn --no-vpn Auto-open an SSH tunnel to the │
│ provisioned droplet when one exists. │
│ --no-vpn skips the tunnel and uses │
│ only the unproxied sources. │
│ [default: vpn] │
│ --verify --no-verify Curl through the proxy once before │
│ fetching and confirm egress is │
│ non-US. │
│ [default: verify] │
│ --hold --no-hold [default: hold] │
│ --help Show this message and exit. │
│ --limit -n <int> [default: 0] │
│ --workers -w <int> Concurrent fetch workers (fallback │
│ tier stays serialized). │
│ [default: 8] │
│ --db <path> [default: │
│ data/zotero/data/zotero.sqlite] │
│ --storage <path> [default: data/zotero/data/storage] │
│ --scratch <path> [default: .state/prisma-fetch] │
│ --proxy <str> Override PRISMA_FETCH_PROXY (else │
│ env). │
│ --vpn --no-vpn Auto-open an SSH tunnel to the │
│ provisioned droplet when one exists. │
│ --no-vpn skips the tunnel and uses │
│ only the unproxied sources. │
│ [default: vpn] │
│ --verify --no-verify Curl through the proxy once before │
│ fetching and confirm egress is non-US. │
│ [default: verify] │
│ --hold --no-hold [default: hold] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

14
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@@ -1,22 +1,22 @@
---
title: stack prisma flow
sidebar_position: 111
sidebar_position: 112
---
# `stack prisma flow`
```
Usage: stack prisma flow [OPTIONS] NAME
Usage: stack prisma flow [OPTIONS] {name}
Emit the PRISMA 2020 flow diagram from current tag counts.
╭─ Arguments ──────────────────────────────────────────────────────────────────╮
│ * name TEXT Project slug. [required] │
│ * name <str> Project slug. [required] │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --mermaid --text [default: mermaid] │
│ --db PATH [default: data/zotero/data/zotero.sqlite] │
│ --hold --no-hold [default: hold] │
│ --help Show this message and exit. │
│ --mermaid --text [default: mermaid] │
│ --db <path> [default: data/zotero/data/zotero.sqlite] │
│ --hold --no-hold [default: hold] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

14
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@@ -1,23 +1,23 @@
---
title: stack prisma init
sidebar_position: 105
sidebar_position: 106
---
# `stack prisma init`
```
Usage: stack prisma init [OPTIONS] NAME
Usage: stack prisma init [OPTIONS] {name}
Create (or re-load) the project's three Zotero anchor items: criteria,
extraction-template, and the reasons codebook.
╭─ Arguments ──────────────────────────────────────────────────────────────────╮
│ * name TEXT Project slug, e.g. skin-subs. [required] │
│ * name <str> Project slug, e.g. skin-subs. [required] │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --db PATH Zotero SQLite path. │
│ [default: data/zotero/data/zotero.sqlite] │
│ --hold --no-hold [default: hold] │
│ --help Show this message and exit. │
│ --db <path> Zotero SQLite path. │
│ [default: data/zotero/data/zotero.sqlite] │
│ --hold --no-hold [default: hold] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

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@@ -1,6 +1,6 @@
---
title: stack prisma ping-llm
sidebar_position: 107
sidebar_position: 108
---
# `stack prisma ping-llm`

21
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@@ -1,12 +1,12 @@
---
title: stack prisma run
sidebar_position: 113
sidebar_position: 114
---
# `stack prisma run`
```
Usage: stack prisma run [OPTIONS] NAME
Usage: stack prisma run [OPTIONS] {name}
Orchestrate all PRISMA stages in order.
@@ -15,18 +15,17 @@ Usage: stack prisma run [OPTIONS] NAME
exclusions are terminal by design.
╭─ Arguments ──────────────────────────────────────────────────────────────────╮
│ * name TEXT Project slug. [required] │
│ * name <str> Project slug. [required] │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --limit -n INTEGER Same limit applied to every stage. │
│ [default: 0] │
│ --limit -n <int> Same limit applied to every stage. │
│ [default: 0] │
│ --skip-fetch │
│ --skip-extract │
│ --db PATH [default: │
│ data/zotero/data/zotero.sqlite] │
│ --storage PATH [default: │
│ data/zotero/data/storage] │
│ --hold --no-hold [default: hold] │
│ --help Show this message and exit. │
│ --db <path> [default: │
│ data/zotero/data/zotero.sqlite] │
│ --storage <path> [default: data/zotero/data/storage] │
│ --hold --no-hold [default: hold] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

38
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@@ -1,34 +1,34 @@
---
title: stack prisma screen
sidebar_position: 108
sidebar_position: 109
---
# `stack prisma screen`
```
Usage: stack prisma screen [OPTIONS] NAME
Usage: stack prisma screen [OPTIONS] {name}
Stage 2 — LLM-driven title/abstract screening pass.
╭─ Arguments ──────────────────────────────────────────────────────────────────╮
│ * name TEXT Project slug. [required] │
│ * name <str> Project slug. [required] │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --limit -n INTEGER 0 = screen every unscreened item. │
│ [default: 0] │
│ --db PATH [default: │
│ data/zotero/data/zotero.sqlite] │
│ --storage PATH [default: data/zotero/data/storage] │
│ --hold --no-hold [default: hold] │
│ --hosts TEXT Comma-separated Ollama base URLs — │
│ fleet mode (#655): parallel │
│ screening via native /api/chat with │
│ per-request num_ctx; bypasses │
│ PRISMA_LLM_* env config. │
│ --fleet-model TEXT Model name on every fleet host. │
│ [default: qwen2.5:14b] │
│ --num-ctx INTEGER Context window per fleet request. │
│ [default: 8192] │
│ --help Show this message and exit. │
│ --limit -n <int> 0 = screen every unscreened item. │
│ [default: 0] │
│ --db <path> [default: │
│ data/zotero/data/zotero.sqlite] │
│ --storage <path> [default: data/zotero/data/storage] │
│ --hold --no-hold [default: hold] │
│ --hosts <str> Comma-separated Ollama base URLs — │
│ fleet mode (#655): parallel │
│ screening via native /api/chat with │
│ per-request num_ctx; bypasses │
│ PRISMA_LLM_* env config. │
│ --fleet-model <str> Model name on every fleet host. │
│ [default: qwen2.5:14b] │
│ --num-ctx <int> Context window per fleet request. │
│ [default: 8192] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

2
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@@ -1,6 +1,6 @@
---
title: stack prisma vpn
sidebar_position: 114
sidebar_position: 115
---
# `stack prisma vpn`

2
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@@ -1,6 +1,6 @@
---
title: stack prisma
sidebar_position: 104
sidebar_position: 105
---
# `stack prisma`

12
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@@ -11,11 +11,11 @@ Usage: stack rec opps [OPTIONS]
Reconcile OPPS calculated rates against Addendum B.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --year -y INTEGER Year to reconcile; omit for all. │
│ --format -f TEXT Output format: md | json. [default: md] │
│ --output -o PATH Write to file instead of stdout. │
│ --tolerance -t INTEGER Cents of tolerance for an 'exact' match. │
│ [default: 0] │
│ --help Show this message and exit. │
│ --year -y <int> Year to reconcile; omit for all. │
│ --format -f <str> Output format: md | json. [default: md] │
│ --output -o <path> Write to file instead of stdout. │
│ --tolerance -t <int> Cents of tolerance for an 'exact' match. │
│ [default: 0] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

12
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@@ -11,11 +11,11 @@ Usage: stack rec pfs [OPTIONS]
Reconcile PFS calculated fees against carrier_locality.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --year -y INTEGER Year to reconcile; omit for all. │
│ --format -f TEXT Output format: md | json. [default: md] │
│ --output -o PATH Write to file instead of stdout. │
│ --tolerance -t INTEGER Cents of tolerance for an 'exact' match. │
│ [default: 0] │
│ --help Show this message and exit. │
│ --year -y <int> Year to reconcile; omit for all. │
│ --format -f <str> Output format: md | json. [default: md] │
│ --output -o <path> Write to file instead of stdout. │
│ --tolerance -t <int> Cents of tolerance for an 'exact' match. │
│ [default: 0] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

16
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@@ -6,19 +6,19 @@ sidebar_position: 2
# `stack run`
```
Usage: stack run [OPTIONS] NAME
Usage: stack run [OPTIONS] {name}
Execute a named pipeline against the chosen target context.
╭─ Arguments ──────────────────────────────────────────────────────────────────╮
│ * name TEXT Pipeline name (e.g. readmissions). [required] │
│ * name <str> Pipeline name (e.g. readmissions). [required] │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --target TEXT Target context: local, lake, trino, databricks, │
│ spark. │
│ --catalog TEXT Unity Catalog name (overrides config). Implies │
│ target=spark. │
│ --save Save pipeline outputs back to the database. │
│ --help Show this message and exit. │
│ --target <str> Target context: local, lake, trino, databricks, │
│ spark. │
│ --catalog <str> Unity Catalog name (overrides config). Implies │
│ target=spark. │
│ --save Save pipeline outputs back to the database. │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

1
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@@ -37,5 +37,6 @@ Usage: stack [OPTIONS] COMMAND [ARGS]...
│ zot Zotero database maintenance. │
│ prisma LLM-driven PRISMA screening workflow. │
│ mail Maddy mail server (DO + Resend smarthost). │
│ nlm NLM terminology releases and VSAC value sets. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

10
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@@ -6,7 +6,7 @@ sidebar_position: 3
# `stack validate`
```
Usage: stack validate [OPTIONS] [PIPELINE]
Usage: stack validate [OPTIONS] [pipeline]
Verify pipeline output contracts against SQLTable models.
@@ -15,11 +15,11 @@ Usage: stack validate [OPTIONS] [PIPELINE]
without saving anything.
╭─ Arguments ──────────────────────────────────────────────────────────────────╮
│ pipeline [PIPELINE] Pipeline name to validate (all if omitted). │
│ pipeline <str> Pipeline name to validate (all if omitted). │
╰──────────────────────────────────────────────────────────────────────────────╯
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --target TEXT Target context: local, lake, trino, databricks. │
│ [default: local] │
│ --help Show this message and exit. │
│ --target <str> Target context: local, lake, trino, databricks. │
│ [default: local] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

10
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@@ -14,10 +14,10 @@ Usage: stack zot dump-schema [OPTIONS]
FIELD_MAP, and CREATOR_TYPES in ``src/zot/db.py`` verbatim.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --db PATH Default: data/zotero/data/zotero.sqlite │
│ --python --json Emit paste-ready Python literals for zot/db.py │
│ (default) or JSON. │
│ [default: python] │
│ --help Show this message and exit. │
│ --db <path> Default: data/zotero/data/zotero.sqlite │
│ --python --json Emit paste-ready Python literals for zot/db.py │
│ (default) or JSON. │
│ [default: python] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

43
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@@ -0,0 +1,43 @@
---
title: stack zot fetch
sidebar_position: 104
---
# `stack zot fetch`
```
Usage: stack zot fetch [OPTIONS]
Attach an open-access PDF to items that lack a full text.
Per item: every Unpaywall location, then Semantic Scholar, PMC and
Europe PMC — open-access copies only (no DOI? a Crossref title match
first). Items with a PDF/EPUB, deleted items and ``document`` items
are skipped. Every attempt is a ledger line; a miss waits 30 days
unless --retry.
Environment: UNPAYWALL_EMAIL — the contact address Unpaywall requires
(default dev@fhirworx.io).
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --collection <str> Collection name. │
│ --tag <str> Tag name. │
│ --type <str> Item type, e.g. journalArticle, book. │
│ --item <str> One item key. │
│ --all Every eligible item. │
│ --limit <int> Stop after N attempts (0 = all). │
│ [default: 0] │
│ --dry-run Show the DOI and open-access locations │
│ per item; write nothing. Reads only, so │
│ the Zotero desktop keeps running. │
│ --retry Retry items the ledger marked as │
│ misses. │
│ --db <path> │
│ --ledger <path> [default: │
│ data/zotero/fetch_ledger.jsonl] │
│ --hold --no-hold Stop the zotero container while │
│ writing. │
│ [default: hold] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

6
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@@ -11,8 +11,8 @@ Usage: stack zot fix-dates [OPTIONS]
Normalize item timestamps to ISO 8601 + install auto-fix triggers.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --db PATH │
│ --hold --no-hold [default: hold] │
│ --help Show this message and exit. │
│ --db <path> │
│ --hold --no-hold [default: hold] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

6
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@@ -11,8 +11,8 @@ Usage: stack zot fix-fields [OPTIONS]
Remap base-field rows to type-specific fieldIDs; drop orphans.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --db PATH │
│ --hold --no-hold [default: hold] │
│ --help Show this message and exit. │
│ --db <path> │
│ --hold --no-hold [default: hold] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

8
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@@ -11,9 +11,9 @@ Usage: stack zot fix-keys [OPTIONS]
Replace invalid Zotero object keys (0/1/O/lowercase → valid).
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --db PATH │
│ --hold --no-hold [default: hold] │
│ --backup --no-backup [default: backup] │
│ --help Show this message and exit. │
│ --db <path> │
│ --hold --no-hold [default: hold] │
│ --backup --no-backup [default: backup] │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

4
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@@ -15,7 +15,7 @@ Usage: stack zot verify-parity [OPTIONS]
bumps Zotero without regenerating the maps.
╭─ Options ────────────────────────────────────────────────────────────────────╮
│ --db PATH │
│ --help Show this message and exit. │
│ --db <path> │
│ --help Show this message and exit. │
╰──────────────────────────────────────────────────────────────────────────────╯
```

1
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@@ -21,5 +21,6 @@ Usage: stack zot [OPTIONS] COMMAND [ARGS]...
│ fix-fields Remap base-field rows to type-specific fieldIDs; drop │
│ orphans. │
│ verify-parity Check that ``zot.db`` constants match the live Zotero schema. │
│ fetch Attach an open-access PDF to items that lack a full text. │
╰──────────────────────────────────────────────────────────────────────────────╯
```