Task

status: cancelled

• task-arash-20260326-192730-144882 status:cancelled title:Task from /storage2/arash/projects/projio/docs/log/issue/issue-arash-20260326-191057-730671.md
• task-arash-20260326-192619-910126 status:cancelled title:Task from /storage2/arash/projects/projio/docs/log/issue/issue-arash-20260326-191057-730671.md
• task-arash-20260325-213628-615820 status:cancelled title:pipeio_rule_stub (original) — generate Snakemake rule stub from contract spec
• task-arash-20260325-213626-924936 status:cancelled title:pipeio_config_patch (original) — generate config.yml registry + params patch
• task-arash-20260317-234737-279890 status:cancelled title:task

status: done

• task-arash-20260331-175739-980549 status:done title:## Register manuscript MCP tools in notio and projio
• task-arash-20260331-175703-656609 status:done title:## Implement manuscript subpackage in notio: schema, assembly, render, figures,
• task-arash-20260331-175617-644481 status:done title:## Design spec: manuscript as a notio subpackage
• task-arash-20260331-145359-712330 status:done title:Audit pipeio docs against implementation
• task-arash-20260330-180056-943959 status:done title:Audit pixecog preprocess/ieeg and write migration guide to pipeio v2 snakebids app design
• task-arash-20260330-175554-840850 status:done title:Run live MCP integration test against pixecog preprocessing pipeline
• task-arash-20260330-175554-589019 status:done title:Add snakebids app detection to registry_scan (non-breaking)
• task-arash-20260330-175553-676358 status:done title:Save and commit all pipeio changes from 2026-03-30 session
• task-arash-20260330-175233-141709 status:done title:Audit pipeio_run, run_status, run_dashboard, run_kill for datalad run migration plan
• task-arash-20260330-175232-430442 status:done title:Update pipeio specs and CLAUDE.md docs for v2 architectural decisions
• task-arash-20260330-175231-488273 status:done title:Flatten pipe/flow hierarchy to flow + category tag in registry model
• task-arash-20260330-031432-455338 status:done title:Fix 3 pipeio bugs: rule_insert double-wrap, config_patch whitespace, dropped anchor
• task-arash-20260328-200549-976370 status:done title:indexio CLI missing --update flag: The MCP indexio_build(update=True) works bu
• task-arash-20260328-193742-747938 status:done title:Address the 4 open indexio/CLI bug reports filed today
• task-arash-20260328-174922-286397 status:done title:## Add MCP tool for biblio graph expansion
• task-arash-20260328-145743-373331 status:done title:Migrate graph.py OpenAlex reference expansion to projio biblio
• task-arash-20260328-011427-733990 status:done title:## Bug: projio note_read tool requires path param but note_list only returns m
• task-arash-20260327-155924-559955 status:done title:## codio: three bugs in codio_rag_sync + unclear MCP docs
• task-arash-20260326-174032-983094 status:done title:MCP tools missing for index setup and source registration
• task-arash-20260326-143012-175237 status:done title:**Feature request: biblio-gui should resolve git-annex symlinks when serving fil
• task-arash-20260326-142950-256126 status:done title:biblio-gui should resolve git-annex symlinks when serving files

status: open

• task-arash-20260331-175508-399347 status:open title:## Register manuscripto in projio: MCP tools, submodule, optional dependency
• task-arash-20260331-175439-058148 status:open title:## Implement manuscripto core: assembly, render, and notio section type
• task-arash-20260318-022253-067748 status:open title:Debug worklog-projio agent_instructions integration

status: pending

• task-arash-20260401-043426-424405 status:pending title:Flatten pipe/flow: update docs paths, collection, modkey, and agent instructions
• task-arash-20260401-043425-765707 status:pending title:Flatten pipe/flow: update projio wrappers and MCP server registration
• task-arash-20260401-043424-875406 status:pending title:Flatten pipe/flow: update pipeio CLI commands
• task-arash-20260401-043424-441698 status:pending title:Flatten pipe/flow: update all pipeio MCP functions
• task-arash-20260401-043322-873085 status:pending title:Flatten pipe/flow to flow-only: registry schema and core model
• task-arash-20260331-231724-488753 status:pending title:Implement pipeio flow rename with modkey.bib citekey update
• task-arash-20260329-230343-774295 status:pending title:codio_func_doc — MCP tool to return function signature + docstring from any installed package
• task-arash-20260328-092458-062195 status:pending title:Task from 20260327-141523-996883
• task-arash-20260326-232759-001222 status:pending title:Implement notio reindex — generate/update index
• task-arash-20260326-232745-588139 status:pending title:Implement pipeio
• task-arash-20260326-192823-764620 status:pending title:Task from /storage2/arash/projects/projio/docs/log/issue/issue-arash-20260326-191057-730671.md
• task-arash-20260326-175901-417280 status:pending title:Add background/async mode to biblio_docling MCP tool
• task-arash-20260326-175857-274269 status:pending title:Slim notio note types to 4 core + add series/refs frontmatter
• task-arash-20260326-151605-074511 status:pending title:docling output not automatically standardized into ref-md markdown
• task-arash-20260325-213617-232334 status:pending title:pipeio_nb_exec — execute notebook via papermill with param injection
• task-arash-20260325-213616-098510 status:pending title:pipeio_log_parse — structured Snakemake log parsing
• task-arash-20260325-213614-991660 status:pending title:pipeio_cross_flow — cross-pipeline registry chain tracking
• task-arash-20260325-213613-854894 status:pending title:pipeio_dag — query rule dependency graph
• task-arash-20260325-213612-674731 status:pending title:pipeio_completion — per-session completion tracking
• task-arash-20260325-213611-387369 status:pending title:pipeio_run + pipeio_run_status + pipeio_run_dashboard — managed Snakemake execution via screen
• task-arash-20260325-213605-945475 status:pending title:pipeio_mod_create — scaffold a new pipeline mod
• task-arash-20260325-213513-640722 status:pending title:pipeio_nb_analyze — extract processing contract from a notebook
• task-arash-20260325-213439-574854 status:pending title:pipeio_config_patch — snakebids-aware config.yml read/write
• task-arash-20260325-213420-015848 status:pending title:pipeio_rule_list + pipeio_rule_stub — Snakemake rule introspection and generation
• task-arash-20260318-000146-662952 status:pending title:Update mkdocs nav and tutorial indexes for all new tutorials
• task-arash-20260318-000144-504496 status:pending title:Tutorial: Site and docs workflow (site detect/serve/stop, chatbot, GitHub Pages)
• task-arash-20260318-000136-985155 status:pending title:Tutorial: Agent orchestration (multi-tool MCP session, full worklog-ready loop)
• task-arash-20260318-000133-499949 status:pending title:Tutorial: Semantic search pipeline (indexio corpus build, rag_query, multi-query)
• task-arash-20260318-000131-385430 status:pending title:Tutorial: Note-driven workflow (notio create/search/update + agent note triage)
• task-arash-20260318-000129-436019 status:pending title:Tutorial: Ecosystem overview (install, init workspace, connect MCP, verify tools)
• task-arash-20260318-000127-440315 status:pending title:Makefile: add DataLad subdataset management targets (pull-origin, push-origin, push-gitlab, pull-gitlab)
• task-arash-20260318-000125-085964 status:pending title:Publish prep: rename codio to codio-tools, bump versions, publish all subpackages + projio

status: queued

• task-arash-20260331-173957-317788 status:queued title:DAG SVG export to docs + pipeio_docs_build convenience tool

status: scheduled

• task-arash-20260331-175356-958039 status:scheduled title:## Scaffold manuscripto package under packages/
• task-arash-20260331-175313-566067 status:scheduled title:## manuscripto design spec — architecture and API surface