Reported issues for doiget Desktop Extension

Pod holds 20 of 39 GitHub reports that passed its relevance review. This can include external user reports, maintainer-confirmed bugs, and concrete feature gaps. Treat them as evidence to inspect, not a count of distinct defects.

Back to doiget Desktop Extension.

Most discussed

Discovery-oriented features for agent-driven literature search (paper_search, paper_text, survey macro, MCP loop)

Motivation — agent-driven research-question discovery, not just DOI→PDF

Using doiget from an LLM agent to actually find the question (not just fetch a known DOI), the loop I want to self-complete is:

search → triage → expand(citations) → fetch → read → map/gap-analysis

Today doiget is excellent at the back half (fetch/batch/graph/bib/csl/serve/capabilities), but the front half assumes you already know the DOIs. The gaps below are what would let an agent run the whol

Read the thread · 2026-06-04 · closed · 3 comments

mcp: align tool output shapes with the CLI --mode json bodies (#204 / #205 mirror)

Purpose

#204 added --mode json bodies for the six human-table CLI commands and #205 added the ERRORS.md §3 JSONL shape for batch. The doiget-mcp tools (doiget_info, doiget_search, doiget_audit_log, doiget_batch_fetch, etc.) each have their own output schema today; they predate the CLI JSON bodies and may diverge in field names / nesting from the CLI surface.

Consistency matters because a single LLM agent often consults both (doiget serve for in-session work and `doiget cli

Read the thread · 2026-05-20 · closed · 3 comments

bug(cli): the human denial help suggests both trust flags unconditionally, while the machine path computes which one actually covers the host

Observed on doiget 0.8.9 against the #443/#461 case:

$ doiget fetch 10.1109/tsp.2018.2812747
error[CAPABILITY_DENIED]: … redirect target strathprints.strath.ac.uk not in allowlist …
  = help: that host is not on the allowlist yet; widen it in …/config.toml
          [network] trust_academic_repos = true   # 15 curated academic suffixes
          [network] trust_oa_registries  = true   # DOAJ, SciELO, Zenodo, OSF, HAL
          [[network.additional_hosts]] host = "strathprints.strath.ac.uk

[Read the thread](https://github.com/QAtlasHub/doiget/issues/478) · 2026-08-25 · closed · 2 comments

### oa-publisher allowlist omits major physics OA hosts (APS, SciPost, IOP) — 7/30 niche papers fall to metadata-only

## Summary

Dogfooding a real **finite-temperature MPS** literature collection on a
university box (via the now-working citation graph, #187) batch-fetched 30
DOIs that OpenAlex reports as Open Access. **24 succeeded; 7 were denied**
with `error[CAPABILITY_DENIED]` — the OA PDF *was discovered* but its host
is not in `oa_publisher_allowlist()`
(`crates/doiget-core/src/http.rs`) / `docs/REDIRECT_ALLOWLIST.md` §3.4.

Denied hosts (real Unpaywall `best_oa_location` targets):

| host | count | natur

[Read the thread](https://github.com/QAtlasHub/doiget/issues/193) · 2026-05-18 · closed · 2 comments

### cleanup batch (LOW): s2 dead api_key, dry_run .expect() panics, missing serde(deny_unknown_fields), SCOPE.md count mismatch

**Category: F/D — low-severity cleanup batch** (grouped like #123)

1. **core** `crates/doiget-core/src/sources/s2.rs:52-53` — `api_key` is `#[allow(dead_code)]`, never sent. Users with a Semantic Scholar key are silently rate-limited to the anonymous tier. Wire the header like APS, or document + warn.
2. **core** `crates/doiget-core/src/dry_run.rs:143,163` — `.expect()` on allowlist lookups panics `doiget plan` if a source key is ever renamed. Convert to `Result<FetchPlan, FetchError>`.
3. **mc

[Read the thread](https://github.com/QAtlasHub/doiget/issues/156) · 2026-05-17 · closed · 2 comments

### Four shipped MCP tools have no entry in MCP_TOOLS.md

Four tools ship in every release binary and have no entry in `docs/MCP_TOOLS.md`:

- `doiget_annotate`
- `doiget_batch_from_bibliography`
- `doiget_paper_tex_source`
- `doiget_tag`

## How this was measured

`doiget serve` run from an installed npm package, `tools/list` compared against the
tool table in `MCP_TOOLS.md` (the rows matching `^| \`doiget_[a-z_]+\``):

live in a shipped oa-only,citation build : 21 (22 after #552) documented in the tool table : 18 explicitly refused,

Read the thread · 2026-08-27 · closed · 1 comment

Ship doiget as a Claude Code plugin: self-hosted marketplace first, then the community catalog

Mechanics verified 2026-08-26 against the installed claude-plugins-official marketplace on disk and the official docs.

Why this and not just `claude mcp add`

A plugin makes installation two lines with no binary handling, and it can carry skills, agents and commands alongside the MCP server — which is where domain workflows (systematic review / PRISMA, etc.) would eventually be delivered.

/plugin marketplace add QAtlasHub/doiget
/plugin install doiget@doiget

Files to add

At t

Read the thread · 2026-08-25 · open · 1 comment

feat(registry): the MCP Registry now documents cargo AND mcpb — the source-only entry can carry packages

server.json has no packages array, so io.github.QAtlasHub/doiget is discoverable in the registry but not installable from it. Verified live:

$ curl 'https://registry.modelcontextprotocol.io/v0/servers?search=doiget'
  name: io.github.QAtlasHub/doiget | version: 0.8.9 | packages: (none)

The reason is recorded in release-plz.yml:

the live MCP Registry does not yet accept the cargo registry type (400 "unsupported registry type: cargo"), though the 2025-12-11 schema lists

Read the thread · 2026-08-25 · closed · 1 comment

Most recent

bug(transport): in a `metadata`-without-`citation` build, every Tier-2 optional source fails UnknownSource

Found while wiring OpenAlex into the optional chain for #461. Not fixed there because it is a different defect with its own blast radius.

The gates disagree

The Tier-2 sources are gated on metadata:

# crates/doiget-core/Cargo.toml
metadata = []
citation = ["metadata"]

resolve_optional_chain is #[cfg(feature = "metadata")], and so are DataCite, Europe PMC, OpenAIRE, HAL and CORE.

Their transport gate is not:

// crates/doiget-cli/src/commands/fetch.rs:267
#[c

[Read the thread](https://github.com/QAtlasHub/doiget/issues/516) · 2026-08-26 · closed · 0 comments

### docs/INTEGRATION: all six host guides are Phase 3 placeholders that tell users to stop and wait — for a phase that shipped

A user who follows `README.md:51` to the host-integration guides is actively told not to proceed.

## Measured 2026-08-26

Every file in `docs/INTEGRATION/` carries the same banner and two unfilled TODOs:

claude-code.md Status: PLACEHOLDER (Phase 3) TODOs: 2 claude-desktop.md Status: PLACEHOLDER (Phase 3) TODOs: 2 cursor.md Status: PLACEHOLDER (Phase 3) TODOs: 2 codex.md Status: PLACEHOLDER (Phase 3) TODOs: 2 obsidian.md Status: PLA

Read the thread · 2026-08-25 · closed · 0 comments

Publish doiget to npm so the MCP entry is one line — optionalDependencies, no postinstall, Trusted Publishing

The concrete build-out of #501's priority-1 channel. Registration mechanics verified 2026-08-26.

Target

claude mcp add doiget -- npx -y doiget serve

No binary handling, no C toolchain, no PATH edit. This is also the prerequisite for the Claude Code plugin route (sibling issue), whose .mcp.json is exactly {"command":"npx","args":["-y","doiget@latest","serve"]} — the same shape the official firebase plugin ships.

What exists to package

The workspace produces one binary

Read the thread · 2026-08-25 · closed · 0 comments

test: the batch --json and MCP diagnostic wiring points would survive being disconnected

Found in the #468 review. Same shape as #413 / #442 / #454 / #458: the component works, the wiring is untested, and disconnecting it leaves the suite green.

batch `--json`

crates/doiget-cli/src/commands/batch.rs:535 (inside classify_joined) is the only place that threads a real FetchPaperOutcome's attempts into build_jsonl_failure.

Every test that asserts the JSONL record contains attempts / remediation calls build_jsonl_failure directly with hand-built arguments. The o