Command reference¶
Every papio command, generated directly from the binary. Pass --json to any command for structured output; see the user guide for the operational workflow and the configuration reference for policy.
Global flags¶
These flags are available on every command.
| Flag | Type | Default | Description |
|---|---|---|---|
--config |
string |
config TOML path | |
--json |
bool |
false |
emit structured JSON |
papio acquire¶
Submit one paper-acquisition request
| Flag | Type | Default | Description |
|---|---|---|---|
--access-mode |
string |
per-request access-mode override | |
--arxiv |
string |
arXiv ID | |
--author |
stringSlice |
[] |
author (repeatable) |
--auto-import |
bool |
false |
plan and apply zotio import automatically when ready |
--batch |
string |
submit works from a JSONL, RIS, BibTeX, CSL-JSON, or MEDLINE/NBIB file (or - for standard input) | |
--collection |
string |
target Zotero collection name (key when used with --from-zotio) | |
--deny-source |
stringSlice |
[] |
deny this source (repeatable) |
--desired-version |
string |
any |
published, accepted, preprint, or any |
--doi |
string |
DOI | |
--from-digest |
int64 |
0 |
queue pending entries from an alert watch |
--from-zotio |
bool |
false |
queue zotio items missing an attached PDF |
--include-owned |
bool |
false |
with --batch, submit works already carrying a PDF in zotio |
--isbn |
string |
ISBN | |
--keys |
stringArray |
[] |
digest work key to queue (repeatable) |
--label |
string |
query context; also the default target collection when --collection is unset | |
--limit |
int |
25 |
maximum zotio items to queue |
--max-cost |
float64 |
0 |
maximum paid-source cost in USD |
--openalex |
string |
OpenAlex work ID | |
--pmid |
string |
PubMed ID | |
--request-id |
string |
stable idempotency key | |
--resolver |
string |
named institutional OpenURL resolver profile | |
--source |
stringSlice |
[] |
allow only this source (repeatable) |
--title |
string |
work title | |
--wait |
bool |
false |
wait for a terminal or human-action state |
--year |
int |
0 |
publication year |
--zotio-item-key |
string |
existing Zotero item key |
papio actions¶
Inspect required human actions
papio actions list¶
List open human actions
| Flag | Type | Default | Description |
|---|---|---|---|
--all |
bool |
false |
include resolved actions |
papio actions open¶
Open the current browser handoff queue
| Flag | Type | Default | Description |
|---|---|---|---|
--dry-run |
bool |
false |
print URLs without opening them |
--limit |
int |
0 |
maximum actions to open (default all) |
papio actions resolve¶
Accept or reject a parked identity review
| Flag | Type | Default | Description |
|---|---|---|---|
--accept |
bool |
false |
accept the identity review |
--reject |
bool |
false |
reject the identity review |
papio adapter¶
Inspect provider and adapter interactions
papio adapter diagnose¶
Build a sanitized support report for a job
papio artifacts¶
Inspect validated immutable artifacts
papio artifacts get¶
Show a validated artifact
| Flag | Type | Default | Description |
|---|---|---|---|
--sha256 |
bool |
false |
interpret argument as an artifact hash |
papio batch¶
Inspect persisted acquisition batches
papio batch report¶
Join a batch manifest with live acquisition outcomes
| Flag | Type | Default | Description |
|---|---|---|---|
--markdown |
bool |
false |
emit an agent-ready Markdown digest |
papio browser¶
Inspect and switch connected browser sessions
papio browser sessions¶
List browser sessions connected since daemon start
papio browser use¶
Give one browser session the papio offer/handoff flow
| Flag | Type | Default | Description |
|---|---|---|---|
--latest |
bool |
false |
switch to the most recently active pending session |
papio bundle¶
Export validated acquisition bundles
papio bundle export¶
Export an idempotent bundle directory
| Flag | Type | Default | Description |
|---|---|---|---|
-o, --output |
string |
destination directory |
papio config¶
Manage papio configuration
papio config init¶
Write explicit first-run configuration
| Flag | Type | Default | Description |
|---|---|---|---|
--access-mode |
string |
required: conservative, assisted, or delegated | |
--data-dir |
string |
artifact and database directory | |
--email |
string |
contact email for polite APIs | |
--force |
bool |
false |
replace an existing config |
papio daemon¶
Run or control the local acquisition daemon
| Flag | Type | Default | Description |
|---|---|---|---|
--socket |
string |
Unix socket path |
papio daemon status¶
Check the running daemon without autostarting one
papio daemon stop¶
Stop the running daemon without autostarting one
papio doctor¶
Check acquisition readiness and local integrations
| Flag | Type | Default | Description |
|---|---|---|---|
--start |
bool |
false |
autostart the daemon before integration checks instead of diagnosing a stopped one |
papio inbox¶
Show the triage inbox
| Flag | Type | Default | Description |
|---|---|---|---|
--limit |
int |
0 |
maximum items (default 50, maximum 100) |
papio inbox counts¶
Show complete triage inbox counts
papio init¶
Set up papio for a first run
| Flag | Type | Default | Description |
|---|---|---|---|
--attachment-mode |
string |
zotio attachment mode: stored or linked-file | |
--check-updates |
bool |
true |
check for papio and zotio updates once a day via GitHub releases (sends nothing else) |
--email |
string |
contact email for polite API pools | |
--extension-id |
string |
Chrome extension ID allowed to reach the native host, or an unpacked extension folder path (papio computes its ID) | |
--firefox-extension-id |
string |
Firefox add-on ID allowed to reach the native host | |
--institution-url |
string |
library discovery or resolver URL; papio derives the OpenURL base | |
--non-interactive |
bool |
false |
do not prompt; retain existing values unless a flag overrides them |
--openurl-base |
string |
institution OpenURL resolver base URL | |
--proquest-account-id |
string |
ProQuest account id, or a ProQuest URL containing accountid= | |
--shibboleth-entity-id |
string |
Shibboleth IdP entityID for federated login-routing | |
--skip-browser |
bool |
false |
skip Chrome extension and native-host setup |
--zotio-path |
string |
zotio executable path |
papio jobs¶
Inspect and control acquisition jobs
papio jobs cancel¶
Cancel a nonterminal job
papio jobs failures¶
Group acquisition jobs that need attention
| Flag | Type | Default | Description |
|---|---|---|---|
--limit |
int |
50 |
maximum groups (1-200) |
--since |
string |
include jobs updated since a duration or RFC3339 timestamp |
papio jobs get¶
Show one job with events and actions
| Flag | Type | Default | Description |
|---|---|---|---|
--wait |
bool |
false |
wait for completion or human action |
papio jobs list¶
List jobs
| Flag | Type | Default | Description |
|---|---|---|---|
--limit |
int |
100 |
maximum rows (1-500) |
--state |
string |
filter by exact job state |
papio jobs retry¶
Explicitly retry a failed, unavailable, or retry-wait job
papio mcp¶
Serve papio tools and resources over MCP stdio
papio native-host¶
Manage browser native-messaging host registration
papio native-host install¶
Register native-messaging host manifests and the host executable
| Flag | Type | Default | Description |
|---|---|---|---|
--firefox-manifest-dir |
string |
override the Firefox native-messaging manifest directory | |
--manifest-dir |
string |
override the Chrome native-messaging manifest directory |
papio native-host status¶
Report native-messaging host registration state
| Flag | Type | Default | Description |
|---|---|---|---|
--firefox-manifest-dir |
string |
override the Firefox native-messaging manifest directory | |
--manifest-dir |
string |
override the Chrome native-messaging manifest directory |
papio native-host uninstall¶
Remove native-messaging host manifests and the host executable
| Flag | Type | Default | Description |
|---|---|---|---|
--firefox-manifest-dir |
string |
override the Firefox native-messaging manifest directory | |
--manifest-dir |
string |
override the Chrome native-messaging manifest directory |
papio search¶
Search configured discovery backends for scholarly works
| Flag | Type | Default | Description |
|---|---|---|---|
--cited-by |
string |
DOI to find papers it cites (backward references; OpenAlex cited_by: filter) | |
--cites |
string |
DOI to find papers citing it (forward citations; OpenAlex cites: filter) | |
--limit |
int |
20 |
maximum results (1-50) |
--new-only |
bool |
false |
omit works already in your library; filters after --limit and may return fewer results |
--oa-only |
bool |
false |
return only open-access works |
--related-to |
string |
DOI to find OpenAlex-related papers (related_to: filter) | |
--source |
string |
discovery backend: openalex or semanticscholar (default: all configured) | |
--year-from |
int |
0 |
minimum publication year |
--year-to |
int |
0 |
maximum publication year |
papio status¶
Show active and recent acquisition jobs
| Flag | Type | Default | Description |
|---|---|---|---|
--follow |
bool |
false |
refresh every 2 seconds |
papio version¶
Print version information
papio watch¶
Manage scheduled discovery watchlists
papio watch add¶
Add a scheduled discovery watch
Add a scheduled discovery watch. Backfill watches take no query. Alert-mode discovery watches report new works without acquiring them.
| Flag | Type | Default | Description |
|---|---|---|---|
--cadence |
string |
daily |
daily, weekly, or Nh |
--cited-by |
string |
DOI to find papers it cites (backward references; OpenAlex cited_by: filter) | |
--cites |
string |
DOI to find papers citing it (forward citations; OpenAlex cites: filter) | |
--collection |
string |
zotio collection for queued papers | |
--kind |
string |
discovery |
watch kind: discovery or backfill |
--label |
string |
human label (defaults to query) | |
--limit-per-run |
int |
10 |
maximum new papers queued per run (1-50) |
--mode |
string |
acquire |
discovery mode: acquire or alert |
--oa-only |
bool |
false |
return only open-access works |
--related-to |
string |
DOI to find OpenAlex-related papers (related_to: filter) | |
--year-from |
int |
0 |
minimum publication year |
--year-to |
int |
0 |
maximum publication year |
papio watch digest¶
Show recently reported works from an alert watch
| Flag | Type | Default | Description |
|---|---|---|---|
--limit |
int |
100 |
maximum digest entries to show (1-500) |
papio watch digest clear¶
Clear pending works from an alert watch digest
papio watch list¶
List scheduled discovery watches
papio watch remove¶
Remove a scheduled discovery watch
papio watch run¶
Force-run a scheduled discovery watch now
papio zotio¶
Preview and apply Zotero integration through zotio
papio zotio apply¶
Apply one immutable zotio plan after SHA-256 confirmation
| Flag | Type | Default | Description |
|---|---|---|---|
--confirm-sha256 |
string |
Exact confirmation SHA-256 printed by papio zotio plan |
papio zotio plan¶
Export ready jobs and preview exact zotio mutations
papio zotio preflight¶
Verify the configured zotio version and capabilities
papio zotio tags¶
Manage the exception-tag ledger on linked Zotero items
papio zotio tags reconcile¶
Converge papio:needs-action / papio:unavailable tags with current job states