Task¶
open (3)¶
Register manuscripto in projio: MCP tools, submodule, optional dependency
date: 2026-03-31 · status: open · confidence: 1.0
Implement manuscripto core: assembly, render, and notio section type
date: 2026-03-31 · status: open · confidence: 1.0
Debug worklog-projio agent_instructions integration
date: 2026-03-18 · status: open · tags: [projio, worklog, mcp, agent-instructions]
pending (32)¶
Prototype marimo-WASM explorable embedded in handbook chapter 1
date: 2026-05-07 · status: pending · tags: [handbook, marimo, interactive, prototype]
Sketch handbook outline + draft chapter 1 ("Interactivity as a research medium")
date: 2026-05-07 · status: pending · tags: [handbook, writing, chapter-1]
Move Interactive Mathematics deep-research PDF into projio + create handbook reference area
date: 2026-05-07 · status: pending · tags: [handbook, reference, agentic-workshop-2026-09]
Provision teaching/agentic-workshop workspace + register in worklog
date: 2026-05-07 · status: pending · tags: [workshop, infra, agentic-workshop-2026-09]
biblio: pool-aware derivative resolution (docling, grobid, openalex from shared storage)
date: 2026-04-03 · status: pending · tags: [task, biblio, pool, derivatives, architecture]
Implement pipeio flow rename with modkey.bib citekey update
date: 2026-03-31 · status: pending · tags: [task, pipeio, notebook, rename]
codio_func_doc — MCP tool to return function signature + docstring from any installed package
date: 2026-03-29 · status: pending
Task from 20260327-141523-996883
date: 2026-03-28 · status: pending
Implement notio reindex — generate/update index
date: 2026-03-26 · status: pending
date: 2026-03-26 · status: pending
Task from /storage2/arash/projects/projio/docs/log/issue/issue-arash-20260326-191057-730671.md
date: 2026-03-26 · status: pending
Add background/async mode to biblio_docling MCP tool
date: 2026-03-26 · status: pending
Slim notio note types to 4 core + add series/refs frontmatter
date: 2026-03-26 · status: pending
docling output not automatically standardized into ref-md markdown
date: 2026-03-26 · status: pending
pipeio_nb_exec — execute notebook via papermill with param injection
date: 2026-03-25 · status: pending
pipeio_log_parse — structured Snakemake log parsing
date: 2026-03-25 · status: pending
pipeio_cross_flow — cross-pipeline registry chain tracking
date: 2026-03-25 · status: pending
pipeio_dag — query rule dependency graph
date: 2026-03-25 · status: pending
pipeio_completion — per-session completion tracking
date: 2026-03-25 · status: pending
pipeio_run + pipeio_run_status + pipeio_run_dashboard — managed Snakemake execution via screen
date: 2026-03-25 · status: pending
pipeio_mod_create — scaffold a new pipeline mod
date: 2026-03-25 · status: pending
pipeio_nb_analyze — extract processing contract from a notebook
date: 2026-03-25 · status: pending
pipeio_config_patch — snakebids-aware config.yml read/write
date: 2026-03-25 · status: pending
pipeio_rule_list + pipeio_rule_stub — Snakemake rule introspection and generation
date: 2026-03-25 · status: pending
Update mkdocs nav and tutorial indexes for all new tutorials
date: 2026-03-18 · status: pending
Tutorial: Site and docs workflow (site detect/serve/stop, chatbot, GitHub Pages)
date: 2026-03-18 · status: pending
Tutorial: Agent orchestration (multi-tool MCP session, full worklog-ready loop)
date: 2026-03-18 · status: pending
Tutorial: Semantic search pipeline (indexio corpus build, rag_query, multi-query)
date: 2026-03-18 · status: pending
Tutorial: Note-driven workflow (notio create/search/update + agent note triage)
date: 2026-03-18 · status: pending
Tutorial: Ecosystem overview (install, init workspace, connect MCP, verify tools)
date: 2026-03-18 · status: pending
date: 2026-03-18 · status: pending
Publish prep: rename codio to codio-tools, bump versions, publish all subpackages + projio
date: 2026-03-18 · status: pending
scheduled (2)¶
Scaffold manuscripto package under packages/
date: 2026-03-31 · status: scheduled · confidence: 1.0
manuscripto design spec — architecture and API surface
date: 2026-03-31 · status: scheduled · confidence: 1.0
failed (5)¶
Flatten pipe/flow: update docs paths, collection, modkey, and agent instructions
date: 2026-04-01 · status: failed · tags: [task, pipeio, refactor, docs, instructions]
Flatten pipe/flow: update projio wrappers and MCP server registration
date: 2026-04-01 · status: failed · tags: [task, pipeio, refactor, mcp, projio]
Flatten pipe/flow: update pipeio CLI commands
date: 2026-04-01 · status: failed · tags: [task, pipeio, refactor, cli]
Flatten pipe/flow: update all pipeio MCP functions
date: 2026-04-01 · status: failed · tags: [task, pipeio, refactor, mcp]
Flatten pipe/flow to flow-only: registry schema and core model
date: 2026-04-01 · status: failed · tags: [task, pipeio, refactor, registry]
planned (1)¶
OSF integration: manifest, push/pull, registration, preprint
date: 2026-04-16 · status: planned · tags: [osf, publication, doi, integration]
cancelled (5)
Task from /storage2/arash/projects/projio/docs/log/issue/issue-arash-20260326-191057-730671.md
date: 2026-03-26 · status: cancelled
Task from /storage2/arash/projects/projio/docs/log/issue/issue-arash-20260326-191057-730671.md
date: 2026-03-26 · status: cancelled
pipeio_rule_stub (original) — generate Snakemake rule stub from contract spec
date: 2026-03-25 · status: cancelled
pipeio_config_patch (original) — generate config.yml registry + params patch
date: 2026-03-25 · status: cancelled
date: 2026-03-17 · status: cancelled
done (86)
report_build empty-bib edge case: skip bibliography preflight when no citations
date: 2026-04-20 · status: done
Implement quarto-reports phase 1 (report_init + report_build)
date: 2026-04-20 · status: done
Teach _scan_deliverables about deck.yml and .qmd
date: 2026-04-20 · status: done
pipeio_run env resolution bug: _resolve_snakemake_cmd() finds snakemake on PAT
date: 2026-04-14 · status: done
Create pipeio-flow-create skill and pixecog-flow-setup skill
date: 2026-04-10 · status: done
docs_collect: overview.md fix + two-phase export/collect architecture
date: 2026-04-09 · status: done · tags: [task, decision]
note_create MCP tool requires 3 round-trips for agent use: create empty template
date: 2026-04-09 · status: done
Add pipeio.matlab module for MATLAB rule wiring
date: 2026-04-08 · status: done
Scenario book: create index page and update scenario-book.md as overview
date: 2026-04-08 · status: done · tags: [task, questio, scenario-book]
Scenario book: multi-day scheduled research sprint
date: 2026-04-08 · status: done · tags: [task, questio, scenario-book]
Scenario book: unexpected finding leads to new hypothesis
date: 2026-04-08 · status: done · tags: [task, questio, scenario-book]
Scenario book: drafting manuscript results from accumulated evidence
date: 2026-04-08 · status: done · tags: [task, questio, scenario-book]
Scenario book: debugging a cross-flow anomaly
date: 2026-04-08 · status: done · tags: [task, questio, scenario-book]
Scenario book: evaluating a new detection method from recent literature
date: 2026-04-08 · status: done · tags: [task, questio, scenario-book]
Scenario book: reproduce Siapas & Wilson 1998 coupling results
date: 2026-04-08 · status: done · tags: [task, questio, scenario-book]
Update questio-record for mid-loop observation capture
date: 2026-04-08 · status: done · tags: [task, questio, impl, skill]
Implement questio-iterate skill
date: 2026-04-08 · status: done · tags: [task, questio, impl, skill]
Implement questio-investigate skill
date: 2026-04-08 · status: done · tags: [task, questio, impl, skill]
Implement milestone→flow link in questio schema and tools
date: 2026-04-08 · status: done · tags: [task, questio, impl]
Spec: reconcile design.md section 8 with agent-as-judge loop philosophy
date: 2026-04-08 · status: done · tags: [task, questio, spec]
Spec: loop infrastructure — milestone→flow link, mid-loop recording, failure taxonomy
date: 2026-04-08 · status: done · tags: [task, questio, spec]
Spec: questio loop mechanisms — investigate, iterate, orient
date: 2026-04-08 · status: done · tags: [task, questio, spec]
Fix docs_collect scripts.md links outside docs_dir
date: 2026-04-08 · status: done
Fix docs_collect mod docs missing from nav YAML
date: 2026-04-08 · status: done
Fix docs_collect missing notebook index.md
date: 2026-04-08 · status: done
Fix docs_collect index.md vs overview.md duplicate nav
date: 2026-04-08 · status: done
Fix registry_scan has_docs always false
date: 2026-04-08 · status: done
questio phase 3: create questio skills (next, ground, record, report, session)
date: 2026-04-08 · status: done · tags: [task, questio]
questio phase 2: implement questio_status and questio_gap MCP tools
date: 2026-04-08 · status: done · tags: [task, questio]
questio phase 1: implement questio_docs_collect MCP tool
date: 2026-04-08 · status: done · tags: [task, questio]
questio phase 0: add result note type to notio + pixecog
date: 2026-04-08 · status: done · tags: [task, questio]
questio phase 0: create questions.yml and milestones.yml for pixecog
date: 2026-04-08 · status: done · tags: [task, questio]
Commit pipeio find_registry fix + add input stage resolution to PipelineContext
date: 2026-04-07 · status: done
pipeio_nb_exec: python_bin as string breaks subprocess
date: 2026-04-07 · status: done
pipeio_nb_exec: add kernel/env option and fix papermill resolution
date: 2026-04-07 · status: done
pipeio_nb_sync nb2py fails for demo workspace notebooks — "Paired notebook not f
date: 2026-04-06 · status: done
Study: biblio-glutton — reference resolution improvement
date: 2026-04-04 · status: done
Study: Unpaywall/oadoi internals — improve biblio OA cascade
date: 2026-04-04 · status: done
Spec: GROBID citation context — beyond simple citation networks
date: 2026-04-04 · status: done
CLI commands for zotero and pool promote
date: 2026-04-04 · status: done
Register Zotero + pool tools in MCP server and update docs
date: 2026-04-04 · status: done
date: 2026-04-04 · status: done
OpenAlex API P1 fixes from audit
date: 2026-04-04 · status: done
Implement: biblio GUI — OpenAlex outbound links in corpus table
date: 2026-04-03 · status: done
Implement: biblio zotero push-tags — write enrichments back to Zotero
date: 2026-04-03 · status: done
Implement: biblio zotero pull — read items + PDFs from Zotero via API
date: 2026-04-03 · status: done
Implement: biblio pool promote — move project-local papers to a pool
date: 2026-04-03 · status: done
Spec: biblio ↔ Zotero integration model
date: 2026-04-03 · status: done
Spec: biblio enrichment pipeline redesign
date: 2026-04-03 · status: done
Audit: biblio concept tagging vs OpenAlex topic classification — overlap anal
date: 2026-04-03 · status: done
Audit: biblio OpenAlex API usage vs actual API capabilities
date: 2026-04-03 · status: done
Implement Shibboleth SAML login for biblio auth ezproxy --login
date: 2026-04-03 · status: done · tags: [task, biblio, auth, ezproxy]
date: 2026-04-02 · status: done · confidence: 1.0
date: 2026-04-02 · status: done · confidence: 1.0
pipeio: modkey.bib default output to .projio/pipeio/
date: 2026-04-02 · status: done
projio: Update MCP tools and CLAUDE.md for new bib architecture
date: 2026-04-02 · status: done
projio: Ship CSL files and update render paths
date: 2026-04-02 · status: done
biblio: New biblio_compile tool
date: 2026-04-02 · status: done
biblio: Move merge output, config, logs to .projio/biblio/
date: 2026-04-02 · status: done
Spec: Document new bib architecture
date: 2026-04-02 · status: done
date: 2026-04-02 · status: done · confidence: 1.0
date: 2026-04-02 · status: done · confidence: 1.0
date: 2026-04-02 · status: done · confidence: 1.0
date: 2026-04-02 · status: done · confidence: 1.0
Register manuscript MCP tools in notio and projio
date: 2026-03-31 · status: done · confidence: 1.0
Implement manuscript subpackage in notio: schema, assembly, render, figures,
date: 2026-03-31 · status: done · confidence: 1.0
Design spec: manuscript as a notio subpackage
date: 2026-03-31 · status: done · confidence: 1.0
DAG SVG export to docs + pipeio_docs_build convenience tool
date: 2026-03-31 · status: done
Audit pipeio docs against implementation
date: 2026-03-31 · status: done
Audit pixecog preprocess/ieeg and write migration guide to pipeio v2 snakebids app design
date: 2026-03-30 · status: done
Run live MCP integration test against pixecog preprocessing pipeline
date: 2026-03-30 · status: done
Add snakebids app detection to registry_scan (non-breaking)
date: 2026-03-30 · status: done
Save and commit all pipeio changes from 2026-03-30 session
date: 2026-03-30 · status: done
Audit pipeio_run, run_status, run_dashboard, run_kill for datalad run migration plan
date: 2026-03-30 · status: done
Update pipeio specs and CLAUDE.md docs for v2 architectural decisions
date: 2026-03-30 · status: done
Flatten pipe/flow hierarchy to flow + category tag in registry model
date: 2026-03-30 · status: done
Fix 3 pipeio bugs: rule_insert double-wrap, config_patch whitespace, dropped anchor
date: 2026-03-30 · status: done
indexio CLI missing --update flag: The MCP indexio_build(update=True) works bu
date: 2026-03-28 · status: done
Address the 4 open indexio/CLI bug reports filed today
date: 2026-03-28 · status: done
Add MCP tool for biblio graph expansion
date: 2026-03-28 · status: done
Migrate graph.py OpenAlex reference expansion to projio biblio
date: 2026-03-28 · status: done
Bug: projio note_read tool requires path param but note_list only returns m
date: 2026-03-28 · status: done
codio: three bugs in codio_rag_sync + unclear MCP docs
date: 2026-03-27 · status: done
MCP tools missing for index setup and source registration
date: 2026-03-26 · status: done
**Feature request: biblio-gui should resolve git-annex symlinks when serving fil
date: 2026-03-26 · status: done
biblio-gui should resolve git-annex symlinks when serving files
date: 2026-03-26 · status: done