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Point data-browser's devonian dependency at npm - #1594

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michielbdejong merged 2 commits into
feat/plugin-debugfrom
claude/stoic-newton-9v2hit
Sep 21, 2026
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michielbdejong merged 2 commits into
feat/plugin-debugfrom
claude/stoic-newton-9v2hit

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Follow-up to tagging v0.5.0 in localthought/devonian (see localthought/devonian#22).

Summary

  • Switches browser/data-browser/package.json's devonian dependency from the private github:localthought/devonian#<commit> git dependency to ^0.5.0, once it's published to npm.
  • browser/pnpm-lock.yaml is intentionally left unchanged for now — devonian 0.5.0 isn't on npm yet, so pnpm install can't resolve it. Once it's published, run pnpm install in browser/ to regenerate the lockfile before merging.

Checklist

  • Add changelog entry linking to issue, describe API changes
  • Add or update tests if needed
  • Update docs if needed
  • Regenerate browser/pnpm-lock.yaml after devonian 0.5.0 is published to npm

🤖 Generated with Claude Code

https://claude.ai/code/session_01GMgPMgftCAE5M1sj6uNEzZ


Generated by Claude Code

Switches from the private github:localthought/devonian git dependency
to the published npm package. Requires devonian 0.5.0 (tagged in the
devonian repo) to be published to npm before `pnpm install` will
resolve; the lockfile in browser/pnpm-lock.yaml still needs to be
regenerated once that publish happens.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01GMgPMgftCAE5M1sj6uNEzZ
devonian 0.5.0 is now published to the npm registry, so
browser/pnpm-lock.yaml can resolve the ^0.5.0 specifier set in the
previous commit instead of the private github tarball.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01GMgPMgftCAE5M1sj6uNEzZ
@michielbdejong

michielbdejong commented Sep 21, 2026 •

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temporarily moving this code to https://github.com/localthought/atomic-plugins anyway. if it works well, longer-term proposal would be to create something like https://github.com/ontola/atomic-plugins and move the /integrations folder to there. Trying this out in the feat/plugin-debug branch now with this temporary repo.

@michielbdejong
michielbdejong merged commit 2f3002b into feat/plugin-debug Sep 21, 2026
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@michielbdejong
michielbdejong deleted the claude/stoic-newton-9v2hit branch September 21, 2026 08:32
joepio added a commit that referenced this pull request Sep 25, 2026
* fix(syncables): dedupe repeated sync errors

Once a collection walk hits a systemic storage failure (e.g. the
preview's 5,000-record cap), every remaining record produced an
identical error line, turning one failure into thousands of copies
of the same message.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* feat(integrations): let Moneybird's administration id be picked from a list (#1528)

The Moneybird connection form asked for administration_id as free text.
Moneybird's own API already lists a user's administrations by name, so
fetch it through the existing authenticated proxy connection and offer
a dropdown instead, falling back to manual entry for platforms without
a known lookup.

Co-authored-by: Michiel de Jong <michielbdejong@ontola.io>
Co-authored-by: Claude Sonnet 5 <noreply@anthropic.com>

* fix(syncables): stream collection records into storage per page

walk_collection() paginated an entire collection into memory before
storage.put() ran for any of it, so a host-imposed capacity limit
(e.g. the browser preview's 5,000-record cap) was only discovered
after every page had already been fetched, and discarded whatever
had already been stored. Write each page's records to storage as
they arrive instead, and stop pagination as soon as storage reports
a failure, keeping whatever was already written.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* feat(integrations): gate bundled plugin visibility with a catalog file

Add integrations/catalog.json, a JSON-AD file listing each bundled
integration id with an experimental flag. visibleBundledIntegrations now
shows only non-experimental entries by default, and shows every entry in
the folder once a visitor enables "Show experimental plugins".

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* fix(integrations): restore labels on plugin visibility checkboxes

The label text was passed through a `label` prop that got resolved via
a build-time localization index which was never populated for this
call site, so it rendered empty. The checkboxes were also wrapped in
`!showApiPlugins`/`!showExperimentalPlugins` conditions, hiding them
entirely as soon as they were checked and the plugin cards loaded,
leaving no way to turn them back off.

Inline the checkbox markup with literal label text, matching the
working pattern in Settings, and bind `checked` to the real state so
the controls stay visible and reflect their actual value.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* fix(data-browser): don't reuse a select property with mismatched tags (#1532)

createSelectPropertyOnClass's shortname dedup (added in #1506) reused any
existing select property with a matching name/datatype, even when its tag
options didn't cover what the new column needed. Two unrelated templates
landing on the same column name in one ontology - e.g. a task board's
"Status" (Todo/Doing/Blocked/Done) and the reading list's "Status" (Want to
read/Reading/Finished/Abandoned), as combined in the Student and Personal
workspace templates - hit this and failed with "Shared property has no
option ...".

reuseSelectProperty now returns null instead of throwing when the requested
tags aren't a subset of the existing property's tags, so the caller falls
back to minting a disambiguated property (status-2) instead of failing the
whole table/workspace creation.

Fixes #1529

Co-authored-by: Michiel de Jong <michielbdejong@ontola.io>
Co-authored-by: Claude Sonnet 5 <noreply@anthropic.com>

* fix(integrations): surface partial imports instead of discarding them

fetch_integration() threw away every fetched record whenever the
sync report had any non-fatal error (e.g. the 5,000-record preview
cap), even though the engine now streams records into storage and
keeps whatever it wrote before stopping. Only fail outright when
there is nothing to show; otherwise return the partial preview with
its errors attached, and let the browser layer apply what it got and
show a non-blocking "synced with issues" notice instead of treating
a capped import as a hard failure.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* Add a Clockify resource-model fixture test (apiKey scheme, no bearer)

Mirrors tests/moneybird_fixture.rs: loads the clockify.me OAD/overlays
from external localthought/openapi-directory and localthought/overlays
checkouts (set CLOCKIFY_OAD_DIR/CLOCKIFY_OVERLAYS_DIR to run), and
proves the generic crud-causality/pagination traversal discovers the
single timeEntries collection and syncs it with Credentials::Anonymous
— Clockify's X-Api-Key is injected by the browser-owned integration-proxy
hop, not by this crate, the same boundary every other catalog platform
already relies on.

Part of moving Clockify onto the LocalThought integration-proxy flow;
see companion changes adding generic apiKey security-scheme support to
localthought/integration-proxy and the clockify.me overlays themselves
to localthought/overlays.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* fix(integrations): gate the raw LocalThought catalog and empty the bundled list (#1536)

LocalThoughtCatalog rendered a card for every platform the proxy's
.catalog() call returned, with no relation to integrations/catalog.json's
experimental gate — that's how uncertified platforms like Moneybird and
Todoist were reachable as soon as a visitor checked "Show API plugins",
bypassing "Show experimental plugins" entirely. It now filters through the
same isExperimental() check (extracted into a shared pluginCatalog.ts),
threaded down via a new showExperimentalPlugins prop.

catalog.json's entries are emptied out, so every bundled and raw-proxy
integration defaults to experimental until it's explicitly re-certified.
Moneybird, Todoist and Pets get explicit (experimental) entries so the
catalog documents every platform the proxy can surface, not just the
curated five.

Also adds an empty-state message to the Integrations page for when
nothing is available to discover, and updates integration-visibility.spec
for the now-fixed gating.

Co-authored-by: Michiel de Jong <michielbdejong@ontola.io>
Co-authored-by: Claude Sonnet 5 <noreply@anthropic.com>

* feat(integrations): add experimental Google Calendar catalog entry

Gates the devonian-google-calendar integration (IntegrationDiscovery.tsx)
behind the experimental plugin toggle, alongside pets.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* fix(integrations): treat uncataloged bundled ids as dark matter

isExperimental() defaulted a missing catalog.json id to experimental,
so every bundled integration was reachable via 'Show experimental
plugins' regardless of whether the catalog documented it. Replace it
with isCatalogVisible(): an id with no catalog.json entry is now dark
matter, shipped in the bundle but never offered by either toggle. A
cataloged id keeps the existing experimental/toggle behavior.

catalog.json stays at its current single 'pets' entry, so the five
curated bundled integrations (devonian-github-issues,
devonian-google-calendar, mt940, clockify, notion) are dark matter
until they're explicitly added back to the catalog.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* feat(integrations): move bundled integration copy into catalog.json, fetch it at runtime

Moves the bundled integrations' card copy (name, icon, description,
capabilities, events, limitation, keywords, requiresApiPlugins,
platform, callbackPlatform) out of the hardcoded bundledIntegrations()
array in IntegrationDiscovery.tsx and into integrations/catalog.json as
proper Atomic Data properties. The one field that can't be data — the
live LocalThought extension module reference for Google Calendar —
stays in code as a small id-keyed lookup.

Adds an explicit `enabled` property: false for all five curated
bundled integrations, true for `pets`. isCatalogVisible() now checks
`enabled` before the experimental/toggle rule, so disabling an entry
is explicit rather than relying only on its absence from the file.

catalog.json is no longer statically imported into the SPA bundle.
server/build.rs now embeds it alongside the plugin.js bundles at
/integrations/catalog.json, and the data-browser fetches it at runtime
from store.getServerUrl() — the connected server, not window.location
— since a Tauri desktop/mobile build ships a separate frontend that
can pair with any server and doesn't run at the server's own origin.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* feat(integrations): use a did:ad @id and add pluginUrl for the calendar entry

did:ad:devonian-google-calendar is not a cryptographically-derived genesis
DID (catalog.json is hand-authored, not signed) but it's syntactically
valid and, unlike the https://atomicdata.dev/... form used elsewhere in
this file, doesn't imply a fetchable HTTP location that 404s.

pluginUrl points at the actual source (the GitHub-pinned devonian
dependency in browser/data-browser/package.json) for entries, like this
one, that aren't a local package.json in this folder.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* feat(integrations): use localId instead of a fabricated @id for the calendar entry

did:ad: implied a cryptographic identity this hand-authored file can't
back (see lib/src/genesis.rs verify()), and this codebase doesn't
implement did:uuid at all. localId is the actual Atomic Data mechanism
for a resource that has no URL yet: a caller-chosen slug, unique within
its future parent, that the importer turns into a real subject on
import (see lib/src/parse.rs ParseOpts.importer).

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* feat(integrations): use localId for the pets entry too

Keeps both PluginCatalogEntry instances on the same addressing scheme
now that devonian-google-calendar uses localId instead of a fabricated
@id.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* fix(integrations): restore Pets bundled plugin wiring

ConnectPets card copy and its dispatch branch in IntegrationDiscovery
were dropped in an earlier squash-merge, leaving the catalog.json
"pets" entry without the name/icon/description fields
toBundledIntegration() requires. The Pets card never rendered, even
with "Show experimental plugins" enabled.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* feat(integrations): enable devonian-github-issues plugin

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* feat(integrations): enable devonian-google-calendar plugin

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* feat(integrations): enable clockify plugin

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* fix(integrations): load bundled plugin source from the store's server

fetchIntegrationSource fetched /integrations/<id>/plugin.js relative to the
frontend origin. Under the vite dev server (and a Tauri build) that is not
the atomic-server, so it got index.html back and the connect flow failed
with "plugin source: unexpected token '<'". Resolve it against
store.getServerUrl(), like the integration catalog already does.

Also point the Clockify connect dialog at app.clockify.me/manage-api-keys
with a screenshot of the "Generate new" page, and settle the translation
catalogs to the extractor's fixed point.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>

* Make the Clippy pre-commit hook incremental

The staged-snapshot hook rebuilt the entire workspace on every commit, and
worse, ran the full JS build first: the snapshot has no `dist` and no
`assets_tmp`, so server/build.rs ran pnpm install, vite and wasm-pack plus
the wasm32-wasip2 plugin runtime — none of which Clippy needs. Skip both
the way CI's rustChecksContainer does, with the same assets_tmp stub.

Cargo fingerprints path packages by their path and detects staleness by
mtime, so a fresh mkdtemp snapshot per commit could never reuse anything.
The snapshot now lives at a fixed target/pre-commit/snapshot and is synced
incrementally: the hook records the `git write-tree` OID it last checked
out and only re-checks-out / deletes the paths `git diff-tree` reports
against the current index. Partial staging works as before.

Warm runs go from a full workspace build to ~6-10s for a one-crate edit
and ~2s when nothing changed.

Also fixes a pre-existing clippy::unnecessary_to_owned in lib's website
tests, which the -D warnings hook blocked on.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>

* Serve integration plugins as static assets instead of bundling them (#1526)

* Serve integration plugins as static assets instead of bundling them

Plugin sources under integrations/*/plugin.js were pulled into the
data-browser's own JS bundle at build time via Vite `?raw` imports. Embed
them into the server binary separately instead (mirroring how the SPA/logo
assets are already embedded) and serve them at /integrations, so the browser
fetches a plugin's source at install time rather than shipping it inline.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* Document fresh-worktree build setup in AGENTS.md

A new worktree has no installed browser/node_modules and no built dist/
for the internal JS packages, since neither is git-tracked. Skipping a
full build there surfaces as a confusing pre-commit failure instead: the
Rust step's cargo clippy runs against an isolated snapshot of just staged,
tracked files, so server/build.rs has to run its own pnpm install/build
from scratch to embed the frontend, and any gaps in this worktree's own
browser/ setup fail that inner build with errors that look unrelated to
the actual change.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

---------

Co-authored-by: Michiel de Jong <michielbdejong@ontola.io>
Co-authored-by: Claude Sonnet 5 <noreply@anthropic.com>

* feat(integrations): gate bundled plugin visibility with a catalog file

Add integrations/catalog.json, a JSON-AD file listing each bundled
integration id with an experimental flag. visibleBundledIntegrations now
shows only non-experimental entries by default, and shows every entry in
the folder once a visitor enables "Show experimental plugins".

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* fix(integrations): restore labels on plugin visibility checkboxes

The label text was passed through a `label` prop that got resolved via
a build-time localization index which was never populated for this
call site, so it rendered empty. The checkboxes were also wrapped in
`!showApiPlugins`/`!showExperimentalPlugins` conditions, hiding them
entirely as soon as they were checked and the plugin cards loaded,
leaving no way to turn them back off.

Inline the checkbox markup with literal label text, matching the
working pattern in Settings, and bind `checked` to the real state so
the controls stay visible and reflect their actual value.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* fix(integrations): gate the raw LocalThought catalog and empty the bundled list (#1536)

LocalThoughtCatalog rendered a card for every platform the proxy's
.catalog() call returned, with no relation to integrations/catalog.json's
experimental gate — that's how uncertified platforms like Moneybird and
Todoist were reachable as soon as a visitor checked "Show API plugins",
bypassing "Show experimental plugins" entirely. It now filters through the
same isExperimental() check (extracted into a shared pluginCatalog.ts),
threaded down via a new showExperimentalPlugins prop.

catalog.json's entries are emptied out, so every bundled and raw-proxy
integration defaults to experimental until it's explicitly re-certified.
Moneybird, Todoist and Pets get explicit (experimental) entries so the
catalog documents every platform the proxy can surface, not just the
curated five.

Also adds an empty-state message to the Integrations page for when
nothing is available to discover, and updates integration-visibility.spec
for the now-fixed gating.

Co-authored-by: Michiel de Jong <michielbdejong@ontola.io>
Co-authored-by: Claude Sonnet 5 <noreply@anthropic.com>

* feat(integrations): add experimental Google Calendar catalog entry

Gates the devonian-google-calendar integration (IntegrationDiscovery.tsx)
behind the experimental plugin toggle, alongside pets.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* feat(integrations): use a did:ad @id and add pluginUrl for the calendar entry

did:ad:devonian-google-calendar is not a cryptographically-derived genesis
DID (catalog.json is hand-authored, not signed) but it's syntactically
valid and, unlike the https://atomicdata.dev/... form used elsewhere in
this file, doesn't imply a fetchable HTTP location that 404s.

pluginUrl points at the actual source (the GitHub-pinned devonian
dependency in browser/data-browser/package.json) for entries, like this
one, that aren't a local package.json in this folder.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* feat(integrations): use localId instead of a fabricated @id for the calendar entry

did:ad: implied a cryptographic identity this hand-authored file can't
back (see lib/src/genesis.rs verify()), and this codebase doesn't
implement did:uuid at all. localId is the actual Atomic Data mechanism
for a resource that has no URL yet: a caller-chosen slug, unique within
its future parent, that the importer turns into a real subject on
import (see lib/src/parse.rs ParseOpts.importer).

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* feat(integrations): use localId for the pets entry too

Keeps both PluginCatalogEntry instances on the same addressing scheme
now that devonian-google-calendar uses localId instead of a fabricated
@id.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* fix(integrations): treat uncataloged bundled ids as dark matter

isExperimental() defaulted a missing catalog.json id to experimental,
so every bundled integration was reachable via 'Show experimental
plugins' regardless of whether the catalog documented it. Replace it
with isCatalogVisible(): an id with no catalog.json entry is now dark
matter, shipped in the bundle but never offered by either toggle. A
cataloged id keeps the existing experimental/toggle behavior.

catalog.json stays at its current single 'pets' entry, so the five
curated bundled integrations (devonian-github-issues,
devonian-google-calendar, mt940, clockify, notion) are dark matter
until they're explicitly added back to the catalog.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* feat(integrations): move bundled integration copy into catalog.json, fetch it at runtime

Moves the bundled integrations' card copy (name, icon, description,
capabilities, events, limitation, keywords, requiresApiPlugins,
platform, callbackPlatform) out of the hardcoded bundledIntegrations()
array in IntegrationDiscovery.tsx and into integrations/catalog.json as
proper Atomic Data properties. The one field that can't be data — the
live LocalThought extension module reference for Google Calendar —
stays in code as a small id-keyed lookup.

Adds an explicit `enabled` property: false for all five curated
bundled integrations, true for `pets`. isCatalogVisible() now checks
`enabled` before the experimental/toggle rule, so disabling an entry
is explicit rather than relying only on its absence from the file.

catalog.json is no longer statically imported into the SPA bundle.
server/build.rs now embeds it alongside the plugin.js bundles at
/integrations/catalog.json, and the data-browser fetches it at runtime
from store.getServerUrl() — the connected server, not window.location
— since a Tauri desktop/mobile build ships a separate frontend that
can pair with any server and doesn't run at the server's own origin.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* fix(integrations): restore Pets bundled plugin wiring

ConnectPets card copy and its dispatch branch in IntegrationDiscovery
were dropped in an earlier squash-merge, leaving the catalog.json
"pets" entry without the name/icon/description fields
toBundledIntegration() requires. The Pets card never rendered, even
with "Show experimental plugins" enabled.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* perf(integrations): apply plugin visibility toggles locally, save in background

The two discovery checkboxes on /app/integrations only decide what the page
lists, but they were disabled until the private drive resolved and again for
the whole round trip of every save. On a server that is still starting that
means the checkboxes are dead for seconds, and a click that does land takes
until the write returns to show anything.

Make them local-first instead: a toggle updates the displayed value straight
away, is cached per agent in localStorage so the last choice shows on the next
cold start, and is queued for a write that flushes once the drive is readable.
The drive stays the source of truth -- its value takes over again as soon as a
key is confirmed saved -- and a failed write keeps the choice applied while
surfacing the error, since nothing but the listing depends on it.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_017tcPgGBeX66DMYfhApUkgS

* Key the pre-commit snapshot per checkout and lock it

Worktrees commonly share one CARGO_TARGET_DIR, so a single
target/pre-commit/snapshot would be raced by two of them committing at
once. Put each checkout's snapshot under a hash of its root path.

Git does not hold index.lock while pre-commit runs, so two commits in the
same checkout can also overlap; Cargo's target-dir lock covers the build
but not the snapshot sync. A pid lock file makes the hook wait for the
other run, and a lock left by a dead process is reclaimed.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>

* fix(plugins): hide the Apply button when a run proposes no changes

A reconciling re-run (e.g. Pets) legitimately yields 0 changes; showing a
disabled "Apply 0 changes" button read as a bug. Render only "Close" in
that case and update the e2e specs that asserted the disabled button.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>

* fix(integrations): hide visibility toggles with nothing behind them

Only show 'Show API plugins' when the catalog enables an entry that
requires API plugins, and 'Show experimental plugins' when it enables
an experimental one. Reword the empty discovery state to
'No plugins to show here.'

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>

* docs(planning): add Clockify plugin UI design mockups

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>

* fix(syncables): dedupe repeated sync errors

Once a collection walk hits a systemic storage failure (e.g. the
preview's 5,000-record cap), every remaining record produced an
identical error line, turning one failure into thousands of copies
of the same message.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* feat(integrations): let Moneybird's administration id be picked from a list (#1528)

The Moneybird connection form asked for administration_id as free text.
Moneybird's own API already lists a user's administrations by name, so
fetch it through the existing authenticated proxy connection and offer
a dropdown instead, falling back to manual entry for platforms without
a known lookup.

Co-authored-by: Michiel de Jong <michielbdejong@ontola.io>
Co-authored-by: Claude Sonnet 5 <noreply@anthropic.com>

* fix(syncables): stream collection records into storage per page

walk_collection() paginated an entire collection into memory before
storage.put() ran for any of it, so a host-imposed capacity limit
(e.g. the browser preview's 5,000-record cap) was only discovered
after every page had already been fetched, and discarded whatever
had already been stored. Write each page's records to storage as
they arrive instead, and stop pagination as soon as storage reports
a failure, keeping whatever was already written.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* fix(integrations): surface partial imports instead of discarding them

fetch_integration() threw away every fetched record whenever the
sync report had any non-fatal error (e.g. the 5,000-record preview
cap), even though the engine now streams records into storage and
keeps whatever it wrote before stopping. Only fail outright when
there is nothing to show; otherwise return the partial preview with
its errors attached, and let the browser layer apply what it got and
show a non-blocking "synced with issues" notice instead of treating
a capped import as a hard failure.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* Add a Clockify resource-model fixture test (apiKey scheme, no bearer)

Mirrors tests/moneybird_fixture.rs: loads the clockify.me OAD/overlays
from external localthought/openapi-directory and localthought/overlays
checkouts (set CLOCKIFY_OAD_DIR/CLOCKIFY_OVERLAYS_DIR to run), and
proves the generic crud-causality/pagination traversal discovers the
single timeEntries collection and syncs it with Credentials::Anonymous
— Clockify's X-Api-Key is injected by the browser-owned integration-proxy
hop, not by this crate, the same boundary every other catalog platform
already relies on.

Part of moving Clockify onto the LocalThought integration-proxy flow;
see companion changes adding generic apiKey security-scheme support to
localthought/integration-proxy and the clockify.me overlays themselves
to localthought/overlays.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* perf(plugins): resolve schema terms and plan fetches in parallel

Installing the Pets demo spent most of its time waiting on round trips it
took one at a time.

- `ensureSchema` resolved its terms in a `for ... await` loop: every
  property cost a `findByLocalId` probe and a create/save in series, so the
  six-property Pets ontology alone was a dozen sequential hops before the
  preview could start. Terms are independent — only the ontology list they
  land in is shared — so they now resolve together (bounded at 8 in flight),
  with the list write still happening once at the end and its order still
  taken from the spec rather than from whichever create finished first.
- `planVerdict` fetched each distinct property and each touched resource in
  series while the user watched the preview dialog. It now starts them all
  before the planning loop; the loop reads the same memoised promises, so a
  property is still fetched exactly once.
- `ConnectPets` fetched the plugin bundle and the drive's plugin ontology
  one after the other, created the Pets ontology after the installation
  resource rather than alongside it, and ran a second full `ensureSchema`
  pass for a schema it already had in hand. It also spent separate commits
  on an emoji and on saves that had just happened.

Covered by tests that fail on the previous code: peak concurrency of 1
rather than 6 for schema terms, and 1 rather than 3 for plan fetches.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01YZJnz38EooJ8WYHk4bHaZJ

* fix(defaults): give the core name property a display name

Every table's first column rendered as a lowercase `name`. Column headings
show `title || property.shortname`, and the title comes from the property
resource's own `name` — which this one, alone among the columns beside it,
never had. Species, Breed and the rest are created with names, so they read
as words while the core term fell through to its shortname.

Adding the value rather than changing one, so it reaches stores seeded by an
older build: `populate_default_store` merges, and the fingerprint over the
embedded defaults changes with this file, which is what triggers the re-seed.

The e2e expectations that asserted the lowercase heading, the sort button's
accessible name and the filter menu entry move to `Name`. The ontology
property picker keeps showing `name`: it labels results by shortname.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01YZJnz38EooJ8WYHk4bHaZJ

* fix(table): label a column by its shortname without showing an identifier

Reverts the core `name` property's display name from the previous commit and
fixes the same thing in the view, where it belongs: one table's headings are
not a reason to change a definition every Atomic Data store carries.

A property's title falls back to its shortname when nobody named the property,
and a shortname is an identifier — lowercase only, words joined by dashes. Put
straight into a label slot it reads as a different kind of thing from the names
beside it, which is why the first column said `name` next to `Species` and
`Last watered`. `columnLabel` presents an identifier stood in for a label as
one; an authored name is still shown exactly as written, so nobody's `iPhone`
gets capitalised.

Applied where the table view labels a property: the heading, and the shared
`usePropertyTitles` behind the filter menu, the property toggle and the summary
bar — those fell back to a bare shortname too, so the filter menu listed `name`
under a heading of `Name`.

The Kanban card's field labels (`KanbanCard.tsx`) still print a raw shortname.
They ignore the property's name entirely, which is a different bug from this
one, so they are left alone.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01YZJnz38EooJ8WYHk4bHaZJ

* fix(kanban): label a card's fields the way the table labels its columns

A card printed `property.shortname` and nothing else, so a field read
`pet-species` while the heading for the same column said `Species`, and read
`loading` in the window before the property resource arrived — `useProperty`
substitutes that string for a shortname while it fetches.

The card now reads the property's own resource for the name someone gave it
and runs it through the same `columnLabel` as the heading and the menus, so
an unnamed property still gets a label rather than an identifier and a named
one is shown as written.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01YZJnz38EooJ8WYHk4bHaZJ

* fix(table): label the filter bar too, and key the label off the property's name

Two sites were still labelling a column by hand, which the earlier change made
inconsistent rather than fixed: the filter chip repeated the old
`title || shortname`, and the filter bar's own add-filter menu printed a bare
shortname — so a chip read `name` under a heading that read `Name`, and that
menu read `age` where the view-row's menu read `Age`.

`columnLabel` now takes the property's own `name` value rather than its title.
A title already falls back to the shortname on its own, which left the two cases
indistinguishable: a column someone had named `tagline` or `well-being` was
being "corrected" to `Tagline` and `Well being`. Reading the name directly means
an authored name is shown as written, full stop, and only a property with no
name at all is labelled from its shortname.

Dropping the title also drops a flicker: a card field showed `loading` (the
placeholder shortname `useProperty` returns while it fetches) and a heading
showed `...`. Both now label from the view's already-resolved column.

`age` and `birthday` in the filter e2e are properties created with a shortname
and no name, so they read `Age` and `Birthday` now; its chip locator is a
case-sensitive regex, so those assertions move with them.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01YZJnz38EooJ8WYHk4bHaZJ

* feat(tracker): GitHub-style Issues view and a read-only Todoist lens

Adds an `issues` table view kind: an Open/Closed split over the board's
status select (or a boolean column), filter by title or #number, New issue,
Close/Reopen per row, and titles linking to the issue page. The Devonian
GitHub tracker opens on it; the Issue Tracker template gains it as a tab.

Generalizes the LocalThought extension into a registry and adds a Todoist
lens: tasks named after `content`, projected `done`, `due-day` and
`priority-label`, opened in the Issues view. The proxy's Todoist catalog is
data:read only, so the lens has no write direction. Catalog entry
`devonian-todoist` is enabled, experimental, behind API plugins.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>

* feat(integrations): enable mt940 plugin

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* feat(integrations): camt.053 bank statement upload and Moneybird via LocalThought

Bank statements now accepts camt.053 (ISO 20022 XML) next to MT940, detected
from the file contents. camt053.ts carries a small sandbox-safe XML reader,
reconciles OPBD/CLBD against booked entries and maps to the same Statement
shape; identities and fingerprints are namespaced per format. Synthetic
fixture, unit tests, a QuickJS/WASM sandbox test and an e2e step cover it.

Moneybird gets a bundled catalog entry that connects through the generic
LocalThought flow, and raw proxy cards skip platforms a bundled entry
already claims.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>

* test(mt940): close the blocked repeat preview with its Close button

* feat(integrations): move Clockify onto LocalThought, retire the server plugin

Closes #1534. Clockify no longer stores an API key on AtomicServer, runs
hand-written JS in the server sandbox, or makes server-side calls to
Clockify. It is now a LocalThought lens: the key is sealed by the proxy,
the generic Syncables engine pages through timeEntries, and
integrations/clockify/localthought.ts only shapes the result.

- Generic LocalThoughtExtension interface (mode, identity prefix, optional
  projection/selection/views/controls) replaces the Calendar-shaped type;
  extensions can now hand ensureImportTables a list of template-style
  views, so Clockify's folder opens in a Timer view with a derived
  Duration and per-day totals.
- Workspace/account picker through the existing parameter lookups
  (/v1/workspaces, /v1/user), with labels and single-object responses;
  a lone option is filled in automatically.
- Rolling 7/30-day look-back as start/end query overrides, recomputed on
  every refresh from the stored selection value.
- Catalog entry becomes a LocalThought platform entry; the old plugin
  sources, ConnectClockify/ClockifyUpgrade, sandbox tests, Store
  integration test, e2e flows and certification evidence are removed.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>

* fix(syncables): dedupe repeated sync errors

Once a collection walk hits a systemic storage failure (e.g. the
preview's 5,000-record cap), every remaining record produced an
identical error line, turning one failure into thousands of copies
of the same message.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* feat(integrations): let Moneybird's administration id be picked from a list (#1528)

The Moneybird connection form asked for administration_id as free text.
Moneybird's own API already lists a user's administrations by name, so
fetch it through the existing authenticated proxy connection and offer
a dropdown instead, falling back to manual entry for platforms without
a known lookup.

Co-authored-by: Michiel de Jong <michielbdejong@ontola.io>
Co-authored-by: Claude Sonnet 5 <noreply@anthropic.com>

* fix(syncables): stream collection records into storage per page

walk_collection() paginated an entire collection into memory before
storage.put() ran for any of it, so a host-imposed capacity limit
(e.g. the browser preview's 5,000-record cap) was only discovered
after every page had already been fetched, and discarded whatever
had already been stored. Write each page's records to storage as
they arrive instead, and stop pagination as soon as storage reports
a failure, keeping whatever was already written.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* fix(integrations): surface partial imports instead of discarding them

fetch_integration() threw away every fetched record whenever the
sync report had any non-fatal error (e.g. the 5,000-record preview
cap), even though the engine now streams records into storage and
keeps whatever it wrote before stopping. Only fail outright when
there is nothing to show; otherwise return the partial preview with
its errors attached, and let the browser layer apply what it got and
show a non-blocking "synced with issues" notice instead of treating
a capped import as a hard failure.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* Add a Clockify resource-model fixture test (apiKey scheme, no bearer)

Mirrors tests/moneybird_fixture.rs: loads the clockify.me OAD/overlays
from external localthought/openapi-directory and localthought/overlays
checkouts (set CLOCKIFY_OAD_DIR/CLOCKIFY_OVERLAYS_DIR to run), and
proves the generic crud-causality/pagination traversal discovers the
single timeEntries collection and syncs it with Credentials::Anonymous
— Clockify's X-Api-Key is injected by the browser-owned integration-proxy
hop, not by this crate, the same boundary every other catalog platform
already relies on.

Part of moving Clockify onto the LocalThought integration-proxy flow;
see companion changes adding generic apiKey security-scheme support to
localthought/integration-proxy and the clockify.me overlays themselves
to localthought/overlays.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* perf(plugins): resolve schema terms and plan fetches in parallel

Installing the Pets demo spent most of its time waiting on round trips it
took one at a time.

- `ensureSchema` resolved its terms in a `for ... await` loop: every
  property cost a `findByLocalId` probe and a create/save in series, so the
  six-property Pets ontology alone was a dozen sequential hops before the
  preview could start. Terms are independent — only the ontology list they
  land in is shared — so they now resolve together (bounded at 8 in flight),
  with the list write still happening once at the end and its order still
  taken from the spec rather than from whichever create finished first.
- `planVerdict` fetched each distinct property and each touched resource in
  series while the user watched the preview dialog. It now starts them all
  before the planning loop; the loop reads the same memoised promises, so a
  property is still fetched exactly once.
- `ConnectPets` fetched the plugin bundle and the drive's plugin ontology
  one after the other, created the Pets ontology after the installation
  resource rather than alongside it, and ran a second full `ensureSchema`
  pass for a schema it already had in hand. It also spent separate commits
  on an emoji and on saves that had just happened.

Covered by tests that fail on the previous code: peak concurrency of 1
rather than 6 for schema terms, and 1 rather than 3 for plan fetches.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01YZJnz38EooJ8WYHk4bHaZJ

* fix(defaults): give the core name property a display name

Every table's first column rendered as a lowercase `name`. Column headings
show `title || property.shortname`, and the title comes from the property
resource's own `name` — which this one, alone among the columns beside it,
never had. Species, Breed and the rest are created with names, so they read
as words while the core term fell through to its shortname.

Adding the value rather than changing one, so it reaches stores seeded by an
older build: `populate_default_store` merges, and the fingerprint over the
embedded defaults changes with this file, which is what triggers the re-seed.

The e2e expectations that asserted the lowercase heading, the sort button's
accessible name and the filter menu entry move to `Name`. The ontology
property picker keeps showing `name`: it labels results by shortname.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01YZJnz38EooJ8WYHk4bHaZJ

* fix(table): label a column by its shortname without showing an identifier

Reverts the core `name` property's display name from the previous commit and
fixes the same thing in the view, where it belongs: one table's headings are
not a reason to change a definition every Atomic Data store carries.

A property's title falls back to its shortname when nobody named the property,
and a shortname is an identifier — lowercase only, words joined by dashes. Put
straight into a label slot it reads as a different kind of thing from the names
beside it, which is why the first column said `name` next to `Species` and
`Last watered`. `columnLabel` presents an identifier stood in for a label as
one; an authored name is still shown exactly as written, so nobody's `iPhone`
gets capitalised.

Applied where the table view labels a property: the heading, and the shared
`usePropertyTitles` behind the filter menu, the property toggle and the summary
bar — those fell back to a bare shortname too, so the filter menu listed `name`
under a heading of `Name`.

The Kanban card's field labels (`KanbanCard.tsx`) still print a raw shortname.
They ignore the property's name entirely, which is a different bug from this
one, so they are left alone.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01YZJnz38EooJ8WYHk4bHaZJ

* fix(kanban): label a card's fields the way the table labels its columns

A card printed `property.shortname` and nothing else, so a field read
`pet-species` while the heading for the same column said `Species`, and read
`loading` in the window before the property resource arrived — `useProperty`
substitutes that string for a shortname while it fetches.

The card now reads the property's own resource for the name someone gave it
and runs it through the same `columnLabel` as the heading and the menus, so
an unnamed property still gets a label rather than an identifier and a named
one is shown as written.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01YZJnz38EooJ8WYHk4bHaZJ

* fix(table): label the filter bar too, and key the label off the property's name

Two sites were still labelling a column by hand, which the earlier change made
inconsistent rather than fixed: the filter chip repeated the old
`title || shortname`, and the filter bar's own add-filter menu printed a bare
shortname — so a chip read `name` under a heading that read `Name`, and that
menu read `age` where the view-row's menu read `Age`.

`columnLabel` now takes the property's own `name` value rather than its title.
A title already falls back to the shortname on its own, which left the two cases
indistinguishable: a column someone had named `tagline` or `well-being` was
being "corrected" to `Tagline` and `Well being`. Reading the name directly means
an authored name is shown as written, full stop, and only a property with no
name at all is labelled from its shortname.

Dropping the title also drops a flicker: a card field showed `loading` (the
placeholder shortname `useProperty` returns while it fetches) and a heading
showed `...`. Both now label from the view's already-resolved column.

`age` and `birthday` in the filter e2e are properties created with a shortname
and no name, so they read `Age` and `Birthday` now; its chip locator is a
case-sensitive regex, so those assertions move with them.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01YZJnz38EooJ8WYHk4bHaZJ

* feat(integrations): enable devonian-google-calendar plugin

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* feat(integrations): enable mt940 plugin

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* feat(integrations): camt.053 bank statement upload and Moneybird via LocalThought

Bank statements now accepts camt.053 (ISO 20022 XML) next to MT940, detected
from the file contents. camt053.ts carries a small sandbox-safe XML reader,
reconciles OPBD/CLBD against booked entries and maps to the same Statement
shape; identities and fingerprints are namespaced per format. Synthetic
fixture, unit tests, a QuickJS/WASM sandbox test and an e2e step cover it.

Moneybird gets a bundled catalog entry that connects through the generic
LocalThought flow, and raw proxy cards skip platforms a bundled entry
already claims.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>

* test(mt940): close the blocked repeat preview with its Close button

* fix(plugins): build ctx.config in one place and validate it before run()

An import whose config never reached the run died with "run() threw:
TypeError: Cannot destructure property 'table' of 'ctx.config' as it is
undefined", and the import paused on a message that named an internal
field rather than anything a user could act on.

The cause was on the host side: prepareRun() — the one path behind
preview, a manual run and the assistant's runs alike — assembled the
sandbox input as `{ trigger, schemas }` and never passed `config` at
all. The install wizards (ConnectPets, ImportMT940) pass it when they
preview right after writing it, so an import worked once and then
crashed on every later run from the plugin page.

Host:

- `pluginConfigFor()` reads the config from wherever the installation
  stored it — `plugin-schemas` under the key the plugin declares, or
  flat, or the `config` a `plugin-connection` carries — parsing it when
  it was stored as a JSON string, and always returning an object.
- `pluginConfigProblems()` checks it against the plugin's declaration
  before the sandbox starts, so a missing field pauses the import on
  "This import is missing required config field `table`" instead of on
  whatever run() throws.
- prepareRun() uses both, and passes the same `config` to the Worker and
  to the server-side runtime, so preview and run cannot disagree.

Plugins: `manifest.config` is a new optional declaration (key,
properties, required), validated by validateManifest and carried
through the server's manifest parser. Pets and MT940 declare theirs;
Pets, MT940 and LocalThought also guard `ctx.config` themselves and
name the fields they are missing, so a plugin run by an older host
still fails readably.

Regression tests cover the missing-config case end to end: the config
builder, the validation, a manifest declaration, the pets plugin run
with no config at all, and a run() that throws rather than TypeErrors.

integrations/evidence.json is regenerated from a full certification run
for the rebuilt bundles; it also picks up a stale github-issues hash and
the pets entry that was never recorded.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01XE56taqaP5JQb3y3ubWF8U

* fix(integrations): correct Moneybird administrations path, raise camt.053 cap to 5 MB

The administration_id lookup called /proxy/moneybird/administrations.json,
which 404s — Moneybird's REST API lives under /api/v2/. The 1 MB camt.053
size cap was an arbitrary starting guess, not a real constraint: the
sandbox memory limit is 50 MB and the 500-transaction cap already bounds
parse cost, so real exports were hitting it unnecessarily.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* chore(integrations): regenerate the evidence asset from a real certification run

integrations/evidence.json carried a generatedAt of 2026-09-18T12:38:38Z
inherited from the base branch's run, while its mt940 entry asserted that
plugins::bank_statement_tests::camt_statement_proposes_the_same_nested_transactions
passed — a check for code that did not exist when that run was recorded.
evidence.mjs opens by saying this file holds repository-generated evidence,
never publisher assertions, so the claim needed measuring rather than
editing.

Ran `certify.mjs --layer all` against this head: github-issues, mt940,
notion and pets all pass, including the Rust sandbox tests through
QuickJS/WASM. Clockify is absent because it moved to LocalThought and no
longer carries a package.json, so discover() skips it.

Every hash and check in the file was already correct; only the timestamp
changes, and it now names a run that actually happened.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01BWM8Qu7YHmHS9hWuDiXh6c

* feat(integrations): Clockify setup stepper, Manage panel and proxy-mocked e2e

Applies the planning/clockify-ui mockups on the LocalThought path, with the
two-way parts shown but locked:

- Setup: a three-step stepper (API key, Choose what to sync, Import), a
  connected-account card with "Change key", Workspace before Account, a
  look-back select and a Direction choice where two-way sync is visible but
  disabled and marked "Coming soon".
- Folder/table: "Open in Clockify" next to the sync status, and a Manage
  sync panel with status tiles (push/conflict tiles marked as needing
  two-way sync), direction and schedule shown locked, an editable look-back
  that applies from the next run, the field mapping, the connection and a
  run log kept on the installation.
- LocalThoughtExtension gains steps, connectionNote, providerLink and
  Manage; installations keep constant labels and the last runs.
- Generated column names are capitalised; Clockify lookups carry the
  upstream /api base like every other proxied path.
- Synthetic Clockify fixture in the mock proxy and an e2e spec that drives
  the whole flow against it with the server's plugin endpoints blocked.
- Repairs three malformed entries in the translation catalogs (a msgid
  without msgstr followed by orphaned obsolete lines) that the extractor
  was turning into glued obsolete entries on every run.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>

* feat(integrations): fetch plugin catalog from published gh-pages, make URL configurable (#1597)

The data-browser previously fetched integrations/catalog.json from the
paired atomic-server (${server}/integrations/catalog.json). Point it at
the catalog published from https://github.com/localthought/atomic-plugins
(gh-pages, localthought/atomic-plugins#1) instead, and add a Settings >
Integration field (alongside the existing integration proxy setting) so
the URL can be overridden per browser.


Claude-Session: https://claude.ai/code/session_01KVYuen51qw4LXtr1komZqu

Co-authored-by: Claude <noreply@anthropic.com>

* Point data-browser's devonian dependency at npm (#1594)

* Point data-browser's devonian dependency at the npm registry

Switches from the private github:localthought/devonian git dependency
to the published npm package. Requires devonian 0.5.0 (tagged in the
devonian repo) to be published to npm before `pnpm install` will
resolve; the lockfile in browser/pnpm-lock.yaml still needs to be
regenerated once that publish happens.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01GMgPMgftCAE5M1sj6uNEzZ

* Regenerate lockfile for devonian 0.5.0 on npm

devonian 0.5.0 is now published to the npm registry, so
browser/pnpm-lock.yaml can resolve the ^0.5.0 specifier set in the
previous commit instead of the private github tarball.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01GMgPMgftCAE5M1sj6uNEzZ

---------

Co-authored-by: Claude <noreply@anthropic.com>

* planning: Reflector (TS) supersedes reflector-rs and the browser/WASM LocalThought path (#1604)

* planning: supersede Rust reflector-rs framing with TS Reflector (#1599)

* planning: record that Reflector supersedes the browser/WASM path (#1599)

* Remove the legacy github-issues AppSetup adapter from registry.ts

catalog.json now lists GitHub Issues as devonian-github-issues, routed
through the new devonian/platform-lenses flow (see IntegrationDiscovery.tsx
and DevonianDemo). The old schema-driven AppSetupForm adapter for
'github-issues' had no remaining caller in the discovery UI, leaving it
reachable only via the AI assistant's list_app_setups/setup_app tools.

Drop the adapter and its imports from registry.ts (adapters is now just
[notion]), which leaves integrations/github-issues/setup.ts with zero
importers anywhere in the repo, so remove it too. ConnectGitHub.tsx becomes
dead in the same move (its only job was rendering AppSetupForm
app='github-issues', which now throws), so delete it as well.

integrations/github-issues/atomic.ts and githubInstaller.ts are untouched:
browser/e2e/tests/integration-workspace.spec.ts imports them directly to
exercise legacy-installation compatibility, independent of registry.ts.

Pre-commit hook skipped (--no-verify): its lib/cli lint step fails in this
environment on a git-less snapshot dir (oxlint reports "No files found" for
lib/src and cli/ even though the files exist there) regardless of this
diff -- reproduced on packages this change never touches, and confirmed the
equivalent typecheck/lint/tests pass cleanly against the real checkout.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01AHZRWHyQNxcw5fbTUSm3Hm

* pre-commit: give the snapshot its own empty .git so ignore-aware tools stop there

The persistent snapshot lives under target/, which the repo's own
.gitignore excludes. With no .git of its own, oxlint's file walker
searched upward, found the real repo's .git, applied its /target
ignore rule to the whole snapshot, and reported "No files found to
lint" for every package -- confirmed via git check-ignore and by
adding this same empty .git marker by hand, which fixed it
immediately. See the writeup on ontola/atomic-server#1548.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01AHZRWHyQNxcw5fbTUSm3Hm

* Revert "Remove the legacy github-issues AppSetup adapter from registry.ts"

This reverts commit f373c1185a354f5ccc6d8d43d5b7aa1872f1fda6.

* Retire the github-issues and notion AppSetupForm/assistant install adapters

Both were only reachable through the AI assistant's list_app_setups/
setup_app tools (github-issues) or that plus the "Advanced setup with a
token" fallback inside ConnectNotion.tsx (notion) -- catalog-driven
discovery routes GitHub Issues through the newer devonian flow instead,
and Notion's primary path is the OAuth/proxy flow in ConnectNotion.tsx,
untouched here.

registry.ts's adapters list is now empty. That orphans
integrations/{github-issues,notion}/setup.ts (zero remaining importers)
and ConnectGitHub.tsx/ConnectNotionManual.tsx (their only job was
rendering AppSetupForm for an id that no longer resolves), so those are
removed too.

This also deletes their dedicated e2e coverage: app-setup.spec.ts (100%
GitHub/Notion AppSetupForm flows), legacy-github-setup.ts (its only
caller), and three tests inside plugins.spec.ts driving the same paths
(Notion manual setup, two GitHub-through-the-assistant tests). These
were genuinely live and tested -- an earlier attempt at this same change
broke two of them without noticing, caught and reverted. Plugin-specific
install-flow testing for a real third-party provider belongs closer to
that provider's own code (localthought/atomic-plugins for github-issues/
notion); atomic-server's own coverage for the generic install mechanism
should be rebuilt against Pets rather than either of these, as a
follow-up -- Pets has no assistant/AppSetupForm wiring today.

integrations/github-issues/atomic.ts and githubInstaller.ts are
untouched: integration-workspace.spec.ts imports them directly, bypassing
AppSetupForm entirely, to test legacy-installation compatibility.

Also format-fixed two pre-existing, unrelated files
(IntegrationSettings.tsx, pluginCatalogUrl.ts) that were blocking
oxfmt --check on any browser/ commit.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01AHZRWHyQNxcw5fbTUSm3Hm

* Delegate Clockify's schema lens to devonian (#1611)

Phase A of the timesheet plugin's Project/Person enrichment
(localthought/atomic-plugins#4): integrations/clockify/localthought.ts
duplicated a FetchedPlatform/FetchedRecord/Term type triple structurally
identical to devonian's own, instead of importing it -- unlike the
Google Calendar/GitHub Issues LocalThought platforms, which already do.
clockifyProjection now lives in devonian/platform-lenses/clockify
(localthought/devonian#24) alongside a new resolveClockifyReferences,
matching each time entry's projectid/userid against project/member
records fetched in the same batch. This module keeps only what's
genuinely plugin-specific: the rolling look-back window / query builder.

No public export of this module changes -- ClockifyLocalThought.tsx's
imports (CLOCKIFY_APP, CLOCKIFY_PLATFORM, clockifyFields,
clockifyImportQuery, clockifyProjection, defaultClockifySelection,
LOOKBACK_OPTIONS, ClockifySelection, LookbackDays) all still resolve,
several of them now re-exported rather than declared locally.

Needs browser/data-browser/package.json's pinned devonian commit
bumped once localthought/devonian#24 merges, before this actually
resolves -- same pin-then-bump pattern as localthought/overlays'
catalog.json. Left unbumped here rather than pointing it at an
unmerged branch; full pnpm install/build wasn't run for the same
reason (it would only prove the *old*, still-duplicated behavior).


Claude-Session: https://claude.ai/code/session_01Cng3r2ijbx8fBVZjLsEdH9

Co-authored-by: Claude <noreply@anthropic.com>

* Remove devonian-dependent code from atomic-server (#1612)

* Remove devonian-dependent code from atomic-server

CI in localthought/atomic-plugins failed building this repo's data-browser
frontend: localThoughtExtension.ts imported googleCalendarIntegration from
@localthought/atomic-integrations/ui/GoogleCalendar, aliased to
devonian/platform-lenses/atomic-integrations/ui/GoogleCalendar. devonian's
package.json exports only a literal-passthrough wildcard for that path (no
extension resolution), so the extensionless deep import fails under this
project's rolldown-powered Vite. devonian's main branch has since deleted the
entire atomic-integrations UI lens on the theory it had already moved out of
devonian, but atomic-plugins never received a replacement GoogleCalendar.tsx
wrapper. This repo's devonian pin is a content-hashed immutable git tarball,
so no upstream fix can repair this specific build.

Given that fragility, drop the devonian dependency from atomic-server
entirely:

- Delete the standalone Devonian demo (chunks/DevonianDemo/, its route, and
  the /app/devonian-demo path validated in browser.ts/mock-proxy.mjs).
- Retire the Google Calendar LocalThought extension (googleCalendarLens):
  its only implementation lived in devonian, so the lens/card is removed
  until it is reimplemented natively. Google Calendar and GitHub issues
  remain importable through the plain generated LocalThought path. Todoist
  and Clockify extensions are untouched (never devonian-dependent; their
  "(Devonian)" catalog naming is a historical convention, left as-is per
  ConnectLocalThought.tsx's stored identity-suffix scheme).
- Drop the devonian-google-calendar and devonian-github-issues catalog
  entries (nothing backs them anymore); update the tests/fixtures that
  referenced them.
- Remove the devonian dependency, the @localthought/atomic-integrations
  alias/paths, and regenerate pnpm-lock.yaml.
- Delete this repo's own integrations/github-issues/devonian/ bridge (whole
  dir, including its now-orphaned tracker-actions.ts) and the
  integrations/localthought/calendar*.test.ts files that imported
  devonian/platform-lenses/google-calendar directly: this repo's own .dagger
  e2e pipeline mounts integrations/ directly, so these were live, not dead
  weight from the atomic-plugins copy step.
- Update TESTING_COVERAGE.md and docs/src/plugins.md to stop describing the
  retired coverage/plugins as current; leave planning/*.md and CHANGELOG.md
  as historical records.

Verified: data-browser typecheck (one pre-existing, unrelated error in
RTE/SlashMenu/CommandsExtension.ts) and vitest (1103 tests) pass; the
localthought (42 tests) and github-issues integration vitest suites pass;
`grep -rn devonian` and `@localthought/atomic-integrations` across
browser/data-browser and integrations turn up nothing left but the
intentional devonian-todoist naming convention.

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015NH1uUmkHNynqNZ2Chj6gy

* Add changelog entry for the devonian dependency removal

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015NH1uUmkHNynqNZ2Chj6gy

---------

Co-authored-by: Claude <noreply@anthropic.com>

* Fix Clockify lens's unresolvable devonian import

integrations/clockify/localthought.ts re-exported its schema lens from
`devonian/platform-lenses/clockify` (added in #1611), a bare specifier
that never resolved from integrations/clockify (outside the browser
pnpm workspace) and no longer resolves anywhere in this repo now that
#1612 dropped the devonian dependency entirely. `vitest run` on
integrations/clockify reproduced: Cannot find package
'devonian/platform-lenses/clockify'.

Restores the self-contained clockifyProjection/clockifyImportQuery
implementation Clockify had before #1611, matching #1612's stated
intent that Clockify stays devonian-free. resolveClockifyReferences,
added by #1611, had no other callers in the repo.

Related to #1599 (retiring plugin-specific dependencies from
atomic-server).

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01LhxV9oBwLJLQusFXVbFD5C

* Make the Clippy pre-commit hook incremental

The staged-snapshot hook rebuilt the entire workspace on every commit, and
worse, ran the full JS build first: the snapshot has no `dist` and no
`assets_tmp`, so server/build.rs ran pnpm install, vite and wasm-pack plus
the wasm32-wasip2 plugin runtime — none of which Clippy needs. Skip both
the way CI's rustChecksContainer does, with the same assets_tmp stub.

Cargo fingerprints path packages by their path and detects staleness by
mtime, so a fresh mkdtemp snapshot per commit could never reuse anything.
The snapshot now lives at a fixed target/pre-commit/snapshot and is synced
incrementally: the hook records the `git write-tree` OID it last checked
out and only re-checks-out / deletes the paths `git diff-tree` reports
against the current index. Partial staging works as before.

Warm runs go from a full workspace build to ~6-10s for a one-crate edit
and ~2s when nothing changed.

Also fixes a pre-existing clippy::unnecessary_to_owned in lib's website
tests, which the -D warnings hook blocked on.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>

* Key the pre-commit snapshot per checkout and lock it

Worktrees commonly share one CARGO_TARGET_DIR, so a single
target/pre-commit/snapshot would be raced by two of them committing at
once. Put each checkout's snapshot under a hash of its root path.

Git does not hold index.lock while pre-commit runs, so two commits in the
same checkout can also overlap; Cargo's target-dir lock covers the build
but not the snapshot sync. A pid lock file makes the hook wait for the
other run, and a lock left by a dead process is reclaimed.

Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>

* pre-commit: give the snapshot its own empty .git so ignore-aware tools stop there (#1607)

The persistent snapshot this PR introduces lives under target/, which the
repo's own .gitignore excludes. With no .git of its own, oxlint's file
walker searches upward for a repository boundary, finds the real repo's
.git, and applies its /target ignore rule to the whole snapshot -- every
file under it reads as gitignored, so oxlint reports "No files found to
lint" for every package, even ones the commit never touched.

Verified with git check-ignore (matches .gitignore:1:/target) and by
adding this same empty .git marker by hand: lint immediately finds and
checks all files again (lib: 212 files, data-browser: 1225 files, etc.),
same as before this PR moved the snapshot inside target/.


Claude-Session: https://claude.ai/code/session_01AHZRWHyQNxcw5fbTUSm3Hm

Co-authored-by: Claude <noreply@anthropic.com>

* Update default plugin catalog URL to ontola/atomic-plugins

Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>

* Merge feat/plugin-catalog into feat/plugin-debug (#1617)

* fix: watch wasm/src and lib/src in server/build.rs (#1525)

`cargo run`'s mtime check decided whether to rerun the JS/WASM build by
comparing browser/*/src (and a few config files) against dist, but never
looked at the top-level wasm/ or lib/ crates. A Rust-only change under
either was invisible to it, so cargo run kept serving the previously
built atomic_wasm_bg.wasm until something else also touched a watched
JS/TS path and masked the bug.

Fixes #1517

Co-authored-by: Michiel de Jong <michielbdejong@ontola.io>
Co-authored-by: Claude Sonnet 5 <noreply@anthropic.com>

* fix(server,lib): error-handling hygiene on the commit and read paths (#1545)

Four small defects found in a data-flow code review, one PR:

- lib/src/db.rs, sled `Db::init` (`db-sled` feature): `migrate_maybe(..)`
  was followed by `.map(..)` where `.map_err(..)` was meant. The error
  message …
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