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Code Issues Packages Projects Releases Wiki Activity
991 Commits 10 Branches 5 Tags
6226acff80dea533298cd20c9f2f3f8e344001eb
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113 Commits
Author SHA1 Message Date
Thomas DurieuxandClaude Opus 5.5 643f4b87e9 feat: let authors leave their bibliography unredacted (#941) (#943) 
* feat: let owners leave chosen files unredacted (#941)

Redacting self-citations in a bibliography reveals which papers are the
authors' own. Owners can now pick files whose content is served as
written; file names are still redacted. Patterns follow .gitignore rules.

The form gets a file picker fed by GitHub's tree API, and the terms box
grows with its content and only warns about regex symbols that can stop a
term from matching.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

* fix: honour !patterns, keep picked braces literal, preview unredacted README

- Patterns now apply in order and the last match wins, as in .gitignore,
  so "*.bib" then "!private.bib" excludes private.bib instead of
  preserving every other file.
- Picked paths escape glob characters, braces included, with a
  backslash; "[{]" did not survive brace expansion.
- The README preview drops terms when the README is an unredacted file,
  and refreshes when the list changes.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

* fix: keep rule order when deduplicating unredacted-file patterns

Rules apply in order and the last match wins, so dedupe keeps the last
copy of a repeated pattern instead of the first. The picker also keeps a
plain path in its place when it follows another rule, rather than moving
it to the front as a pick.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

* fix: apply unredacted-file rules to folders, as in .gitignore

A rule that matches a folder now covers every file inside it, so "*.bib"
then "!private" keeps private/refs.bib redacted. A trailing "/" limits a
rule to folders.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

* fix: folder unchecks win over broad rules; accept short commit hashes

- Unchecking a folder that a broader rule such as "*.bib" still covers
  appends a "!/folder/" exclusion, so its files really go back to being
  redacted.
- The tree endpoint accepts the 6+ character hashes the commit field
  allows and resolves them to a full SHA before reading the tree.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

* fix: picker counts folder rules exactly as the server does

Rules ending in "/" stay patterns instead of being read as picked files,
and the checkboxes now run the saved rule list (picks, then patterns)
through the server's matcher, so the dialog cannot show files as
redacted that the server leaves unredacted.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

* fix: insert escaped terms literally in "Match as written"

String.replace expanded "$&", "$'" and "$1" in the term, so the fix
could corrupt the line. Splice by index instead.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

---------

Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
 2026-11-11 14:10:54 +01:00
Thomas Durieux ded6f905fd merge: reconcile paid hosting with latest main 2026-11-02 21:12:29 +00:00
Thomas Durieux 410863d253 feat: add paid author and conference hosting with Stripe 2026-11-02 20:49:03 +00:00
Thomas Durieux 6cf5445972 fix: fill gaps in GitHub Markdown rendering (#912) 
* fix: fill gaps in GitHub Markdown rendering

* fix: harden Markdown dependencies and address review findings
 2026-11-02 07:56:32 +01:00
Thomas Durieux a301c46a94 fix: harden repository content and improve access recovery 
Sandbox executable MIME aliases, enforce strict Mermaid rendering, and add security regression coverage. Upgrade vulnerable dependencies with archive compatibility checks and Node 22/24 CI. Make repository restoration atomic and provide actionable viewer errors with retry controls.
 2026-11-02 05:50:34 +00:00
Thomas Durieux fd0dd0adbd chore(deps): upgrade dependencies and remove production vulnerabilities 2026-10-08 10:21:00 +00:00
dependabot[bot] 1e3a019757 chore(deps-dev): bump smol-toml from 1.6.1 to 1.8.0 
Bumps [smol-toml](https://github.com/squirrelchat/smol-toml) from 1.6.1 to 1.8.0.
- [Release notes](https://github.com/squirrelchat/smol-toml/releases)
- [Commits](https://github.com/squirrelchat/smol-toml/compare/v1.6.1...v1.8.0)

---
updated-dependencies:
- dependency-name: smol-toml
  dependency-version: 1.8.0
  dependency-type: indirect
...

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 2026-09-10 02:55:51 +00:00
tdurieux 984906a89a fix: use public package URLs for clean CI installs 2026-09-09 13:25:36 +02:00
tdurieux 4a18f94631 refactor: migrate the frontend from AngularJS to Vue 3 2026-09-09 13:19:53 +02:00
tdurieux 5fdec8d6f9 fix: keep dependency downloads portable across registries 2026-09-08 16:34:40 +02:00
tdurieux da530d645f fix: clear dependency vulnerabilities without overrides 2026-09-08 16:31:59 +02:00
tdurieux 8ad0ec65f0 chore: upgrade Express to 5.2.1 2026-09-08 16:22:23 +02:00
tdurieux 50d606d0c1 fix: bound regex execution during anonymization 2026-09-06 09:16:48 +02:00
dependabot[bot] f18d2de93c chore(deps-dev): bump @humanfs/node from 0.16.7 to 0.16.8 (#795) 
Bumps [@humanfs/node](https://github.com/humanwhocodes/humanfs/tree/HEAD/packages/node) from 0.16.7 to 0.16.8.
- [Release notes](https://github.com/humanwhocodes/humanfs/releases)
- [Changelog](https://github.com/humanwhocodes/humanfs/blob/main/packages/node/CHANGELOG.md)
- [Commits](https://github.com/humanwhocodes/humanfs/commits/node-v0.16.8/packages/node)

---
updated-dependencies:
- dependency-name: "@humanfs/node"
  dependency-version: 0.16.8
  dependency-type: indirect
...

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 2026-09-03 05:00:33 +02:00
dependabot[bot] 75ce46b70e chore(deps): bump serialize-javascript and mocha (#794) 
Bumps [serialize-javascript](https://github.com/yahoo/serialize-javascript) to 7.1.1 and updates ancestor dependency [mocha](https://github.com/mochajs/mocha). These dependencies need to be updated together.


Updates `serialize-javascript` from 6.0.2 to 7.1.1
- [Release notes](https://github.com/yahoo/serialize-javascript/releases)
- [Commits](https://github.com/yahoo/serialize-javascript/compare/v6.0.2...v7.1.1)

Updates `mocha` from 10.8.2 to 12.0.0
- [Release notes](https://github.com/mochajs/mocha/releases)
- [Changelog](https://github.com/mochajs/mocha/blob/main/CHANGELOG.md)
- [Commits](https://github.com/mochajs/mocha/compare/v10.8.2...v12.0.0)

---
updated-dependencies:
- dependency-name: serialize-javascript
  dependency-version: 7.1.1
  dependency-type: indirect
- dependency-name: mocha
  dependency-version: 12.0.0
  dependency-type: direct:development
...

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 2026-09-02 07:30:19 +02:00
dependabot[bot] 6b27578006 chore(deps): bump sanitize-html from 2.17.5 to 2.17.7 (#793) 
Bumps [sanitize-html](https://github.com/apostrophecms/apostrophe/tree/HEAD/packages/sanitize-html) from 2.17.5 to 2.17.7.
- [Changelog](https://github.com/apostrophecms/apostrophe/blob/main/packages/sanitize-html/CHANGELOG.md)
- [Commits](https://github.com/apostrophecms/apostrophe/commits/HEAD/packages/sanitize-html)

---
updated-dependencies:
- dependency-name: sanitize-html
  dependency-version: 2.17.7
  dependency-type: direct:production
...

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 2026-09-02 07:15:41 +02:00
dependabot[bot] 7298f5cd76 chore(deps): bump brace-expansion (#786) 
Bumps  and [brace-expansion](https://github.com/juliangruber/brace-expansion). These dependencies needed to be updated together.

Updates `brace-expansion` from 1.1.14 to 1.1.18
- [Release notes](https://github.com/juliangruber/brace-expansion/releases)
- [Commits](https://github.com/juliangruber/brace-expansion/compare/v1.1.14...v1.1.18)

Updates `brace-expansion` from 2.1.0 to 2.1.4
- [Release notes](https://github.com/juliangruber/brace-expansion/releases)
- [Commits](https://github.com/juliangruber/brace-expansion/compare/v1.1.14...v1.1.18)

Updates `brace-expansion` from 5.0.5 to 5.0.9
- [Release notes](https://github.com/juliangruber/brace-expansion/releases)
- [Commits](https://github.com/juliangruber/brace-expansion/compare/v1.1.14...v1.1.18)

---
updated-dependencies:
- dependency-name: brace-expansion
  dependency-version: 1.1.18
  dependency-type: indirect
- dependency-name: brace-expansion
  dependency-version: 2.1.4
  dependency-type: indirect
- dependency-name: brace-expansion
  dependency-version: 5.0.9
  dependency-type: indirect
...

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 2026-08-21 09:41:03 +02:00
dependabot[bot] a30457993d chore(deps-dev): bump js-yaml from 4.2.0 to 4.3.1 (#772) 
Bumps [js-yaml](https://github.com/nodeca/js-yaml) from 4.2.0 to 4.3.1.
- [Changelog](https://github.com/nodeca/js-yaml/blob/4.3.1/CHANGELOG.md)
- [Commits](https://github.com/nodeca/js-yaml/compare/4.2.0...4.3.1)

---
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- dependency-name: js-yaml
  dependency-version: 4.3.1
  dependency-type: indirect
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 2026-08-11 00:03:20 +02:00
dependabot[bot] d53aba129e chore(deps): bump sanitize-html from 2.17.4 to 2.17.5 (#767) 
Bumps [sanitize-html](https://github.com/apostrophecms/apostrophe/tree/HEAD/packages/sanitize-html) from 2.17.4 to 2.17.5.
- [Changelog](https://github.com/apostrophecms/apostrophe/blob/main/packages/sanitize-html/CHANGELOG.md)
- [Commits](https://github.com/apostrophecms/apostrophe/commits/sanitize-html@2.17.5/packages/sanitize-html)

---
updated-dependencies:
- dependency-name: sanitize-html
  dependency-version: 2.17.5
  dependency-type: direct:production
...

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 2026-08-07 00:08:30 +02:00
dependabot[bot] 53a8c4d8b3 chore(deps): bump ip-address from 10.2.0 to 10.4.0 (#769) 
Bumps [ip-address](https://github.com/beaugunderson/ip-address) from 10.2.0 to 10.4.0.
- [Release notes](https://github.com/beaugunderson/ip-address/releases)
- [Commits](https://github.com/beaugunderson/ip-address/compare/v10.2.0...v10.4.0)

---
updated-dependencies:
- dependency-name: ip-address
  dependency-version: 10.4.0
  dependency-type: indirect
...

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 2026-08-07 00:08:19 +02:00
dependabot[bot] a8733af4f4 chore(deps): bump mongoose from 7.8.9 to 7.8.10 (#761) 
Bumps [mongoose](https://github.com/Automattic/mongoose) from 7.8.9 to 7.8.10.
- [Release notes](https://github.com/Automattic/mongoose/releases)
- [Changelog](https://github.com/Automattic/mongoose/blob/7.8.10/CHANGELOG.md)
- [Commits](https://github.com/Automattic/mongoose/commits/7.8.10)

---
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- dependency-name: mongoose
  dependency-version: 7.8.10
  dependency-type: direct:production
...

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 2026-07-28 19:38:27 +02:00
dependabot[bot] 188712c5eb chore(deps): bump body-parser from 1.20.5 to 1.20.6 (#762) 
Bumps [body-parser](https://github.com/expressjs/body-parser) from 1.20.5 to 1.20.6.
- [Release notes](https://github.com/expressjs/body-parser/releases)
- [Changelog](https://github.com/expressjs/body-parser/blob/master/HISTORY.md)
- [Commits](https://github.com/expressjs/body-parser/compare/1.20.5...1.20.6)

---
updated-dependencies:
- dependency-name: body-parser
  dependency-version: 1.20.6
  dependency-type: indirect
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 2026-07-28 19:38:16 +02:00
dependabot[bot] d21b84b1b4 chore(deps): bump postcss from 8.5.13 to 8.5.24 (#763) 
Bumps [postcss](https://github.com/postcss/postcss) from 8.5.13 to 8.5.24.
- [Release notes](https://github.com/postcss/postcss/releases)
- [Changelog](https://github.com/postcss/postcss/blob/main/CHANGELOG.md)
- [Commits](https://github.com/postcss/postcss/compare/8.5.13...8.5.24)

---
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- dependency-name: postcss
  dependency-version: 8.5.24
  dependency-type: indirect
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 2026-07-28 19:38:08 +02:00
dependabot[bot] e4e102eccd chore(deps-dev): bump http-proxy-middleware from 3.0.5 to 3.0.7 (#732) 
Bumps [http-proxy-middleware](https://github.com/chimurai/http-proxy-middleware) from 3.0.5 to 3.0.7.
- [Release notes](https://github.com/chimurai/http-proxy-middleware/releases)
- [Changelog](https://github.com/chimurai/http-proxy-middleware/blob/v3.0.7/CHANGELOG.md)
- [Commits](https://github.com/chimurai/http-proxy-middleware/compare/v3.0.5...v3.0.7)

---
updated-dependencies:
- dependency-name: http-proxy-middleware
  dependency-version: 3.0.7
  dependency-type: direct:development
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 2026-06-26 08:05:27 +02:00
dependabot[bot] b98ad338fe chore(deps-dev): bump form-data from 2.5.5 to 2.5.6 (#733) 
Bumps [form-data](https://github.com/form-data/form-data) from 2.5.5 to 2.5.6.
- [Changelog](https://github.com/form-data/form-data/blob/master/CHANGELOG.md)
- [Commits](https://github.com/form-data/form-data/compare/v2.5.5...v2.5.6)

---
updated-dependencies:
- dependency-name: form-data
  dependency-version: 2.5.6
  dependency-type: indirect
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 2026-06-26 08:05:14 +02:00
dependabot[bot] 1a146ea0c7 chore(deps-dev): bump js-yaml from 4.1.1 to 4.2.0 (#734) 
Bumps [js-yaml](https://github.com/nodeca/js-yaml) from 4.1.1 to 4.2.0.
- [Changelog](https://github.com/nodeca/js-yaml/blob/master/CHANGELOG.md)
- [Commits](https://github.com/nodeca/js-yaml/compare/4.1.1...4.2.0)

---
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- dependency-name: js-yaml
  dependency-version: 4.2.0
  dependency-type: indirect
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 2026-06-22 15:23:36 +02:00
dependabot[bot] bdfcc56d81 chore(deps): bump qs and express (#719) 
Bumps [qs](https://github.com/ljharb/qs) to 6.15.2 and updates ancestor dependency [express](https://github.com/expressjs/express). These dependencies need to be updated together.


Updates `qs` from 6.14.2 to 6.15.2
- [Changelog](https://github.com/ljharb/qs/blob/main/CHANGELOG.md)
- [Commits](https://github.com/ljharb/qs/compare/v6.14.2...v6.15.2)

Updates `express` from 4.22.1 to 4.22.2
- [Release notes](https://github.com/expressjs/express/releases)
- [Changelog](https://github.com/expressjs/express/blob/v4.22.2/History.md)
- [Commits](https://github.com/expressjs/express/compare/v4.22.1...v4.22.2)

---
updated-dependencies:
- dependency-name: qs
  dependency-version: 6.15.2
  dependency-type: indirect
- dependency-name: express
  dependency-version: 4.22.2
  dependency-type: direct:production
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 2026-05-23 06:32:36 +03:00
dependabot[bot] d0a1380884 chore(deps): bump sanitize-html from 2.17.3 to 2.17.4 (#717) 
Bumps [sanitize-html](https://github.com/apostrophecms/apostrophe/tree/HEAD/packages/sanitize-html) from 2.17.3 to 2.17.4.
- [Changelog](https://github.com/apostrophecms/apostrophe/blob/main/packages/sanitize-html/CHANGELOG.md)
- [Commits](https://github.com/apostrophecms/apostrophe/commits/HEAD/packages/sanitize-html)

---
updated-dependencies:
- dependency-name: sanitize-html
  dependency-version: 2.17.4
  dependency-type: direct:production
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 2026-05-21 20:46:10 +03:00
dependabot[bot] b03c4b437c chore(deps): bump fast-xml-builder from 1.1.5 to 1.2.0 (#707) 
Bumps [fast-xml-builder](https://github.com/NaturalIntelligence/fast-xml-builder) from 1.1.5 to 1.2.0.
- [Changelog](https://github.com/NaturalIntelligence/fast-xml-builder/blob/main/CHANGELOG.md)
- [Commits](https://github.com/NaturalIntelligence/fast-xml-builder/compare/v1.1.5...v1.2.0)

---
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- dependency-name: fast-xml-builder
  dependency-version: 1.2.0
  dependency-type: indirect
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 2026-05-09 13:31:56 +02:00
tdurieux aae6eae6eb handle rate limit 2026-05-06 17:50:01 +03:00
tdurieux 75b67448ef fix 2026-05-06 11:24:48 +03:00
dependabot[bot]tdurieuxThomas Durieux
 		e34f45522f chore(deps): bump uuid and bullmq (#691) 
* chore(deps): bump uuid and bullmq

Removes [uuid](https://github.com/uuidjs/uuid). It's no longer used after updating ancestor dependency [bullmq](https://github.com/taskforcesh/bullmq). These dependencies need to be updated together.


Removes `uuid`

Updates `bullmq` from 2.4.0 to 5.76.5
- [Release notes](https://github.com/taskforcesh/bullmq/releases)
- [Commits](https://github.com/taskforcesh/bullmq/compare/v2.4.0...v5.76.5)

---
updated-dependencies:
- dependency-name: bullmq
  dependency-version: 5.76.5
  dependency-type: direct:production
- dependency-name: uuid
  dependency-version: 
  dependency-type: indirect
...

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* fix(bullmq): adapt isRunning + getJobs typing for v5 API

Worker.isRunning became a method (was a property in v2), and
Queue.getJobs now requires a mutable JobType[] (was string[]).

* clean up

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Co-authored-by: tdurieux <durieuxthomas@hotmail.com>
Co-authored-by: Thomas Durieux <5577568+tdurieux@users.noreply.github.com>
 2026-05-06 08:40:12 +02:00
tdurieux 2528f42b59 add tests 2026-05-06 08:23:22 +03:00
dependabot[bot] e306adcc97 chore(deps): bump ip-address and socks (#697) 
Bumps [ip-address](https://github.com/beaugunderson/ip-address) and [socks](https://github.com/JoshGlazebrook/socks). These dependencies needed to be updated together.

Updates `ip-address` from 9.0.5 to 10.2.0
- [Commits](https://github.com/beaugunderson/ip-address/commits)

Updates `socks` from 2.8.4 to 2.8.8
- [Release notes](https://github.com/JoshGlazebrook/socks/releases)
- [Commits](https://github.com/JoshGlazebrook/socks/compare/2.8.4...2.8.8)

---
updated-dependencies:
- dependency-name: ip-address
  dependency-version: 10.2.0
  dependency-type: indirect
- dependency-name: socks
  dependency-version: 2.8.8
  dependency-type: indirect
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 2026-05-06 07:21:33 +02:00
dependabot[bot] 78ff8eaa9b chore(deps): bump mongoose from 7.8.4 to 7.8.9 (#698) 
Bumps [mongoose](https://github.com/Automattic/mongoose) from 7.8.4 to 7.8.9.
- [Release notes](https://github.com/Automattic/mongoose/releases)
- [Changelog](https://github.com/Automattic/mongoose/blob/master/CHANGELOG.md)
- [Commits](https://github.com/Automattic/mongoose/commits)

---
updated-dependencies:
- dependency-name: mongoose
  dependency-version: 7.8.9
  dependency-type: direct:production
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 2026-05-06 07:21:17 +02:00
tdurieuxandClaude Opus 4.7 79f555769d improve binary file detection: content sniffing + jsonl support 
Files like .jsonl that mime-types doesn't know fell through to
application/octet-stream and rendered as "Unsupported binary file" in
the viewer. Replace istextorbinary with isbinaryfile for content-based
detection, and use mime-types for name-based classification with a
textual application/* allowlist.

The streaming transformer now defers classification when the name is
inconclusive and sniffs the first chunk before emitting "transform",
so route.ts and AnonymizedFile.ts get a content-aware Content-Type.
Whitelists .jsonl and .ndjson to short-circuit dataset files.

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>
 2026-05-06 07:52:48 +03:00
tdurieux f8c91ca0af multiple fixes 2026-05-05 10:32:31 +03:00
dependabot[bot] 13a7ae9850 chore(deps): bump postcss from 8.5.9 to 8.5.13 (#692) 
Bumps [postcss](https://github.com/postcss/postcss) from 8.5.9 to 8.5.13.
- [Release notes](https://github.com/postcss/postcss/releases)
- [Changelog](https://github.com/postcss/postcss/blob/main/CHANGELOG.md)
- [Commits](https://github.com/postcss/postcss/compare/8.5.9...8.5.13)

---
updated-dependencies:
- dependency-name: postcss
  dependency-version: 8.5.13
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
 2026-05-03 15:34:07 +02:00
tdurieux 1968e3341a 2.3.0 2026-04-24 16:14:29 +02:00
tdurieux 88f826aab4 update design 2026-04-24 14:55:18 +02:00
dependabot[bot] 063f10f18e chore(deps): bump sanitize-html from 2.17.2 to 2.17.3 (#680) 2026-04-17 07:14:28 +02:00
dependabot[bot] c4f153cfa0 chore(deps): bump path-to-regexp and express (#671) 2026-04-15 09:57:31 +02:00
dependabot[bot] 2940f20134 chore(deps-dev): bump brace-expansion from 1.1.11 to 1.1.14 (#677) 2026-04-15 09:57:09 +02:00
dependabot[bot] 85f05cd698 chore(deps): bump picomatch and knip (#673) 2026-04-15 09:54:42 +02:00
dependabot[bot] 7eeb4bed32 chore(deps): bump lodash from 4.17.21 to 4.18.1 (#674) 2026-04-15 09:49:57 +02:00
dependabot[bot] 18dc74784b chore(deps-dev): bump form-data from 2.5.1 to 2.5.5 (#491) 2026-04-15 09:49:27 +02:00
dependabot[bot] 357883b1b2 chore(deps): bump @octokit/request from 8.2.0 to 8.4.1 (#418) 2026-04-15 09:48:00 +02:00
dependabot[bot] 01ddc245c0 chore(deps): bump mongoose from 7.6.10 to 7.8.4 (#414) 2026-04-15 09:47:28 +02:00
dependabot[bot] 2c12fd734a chore(deps): bump unzip-stream from 0.3.1 to 0.3.4 (#319) 2026-04-15 09:46:45 +02:00
Thomas Durieux 8198a4b44a Standardize error responses with consistent format and human-readable messages (#667) 2026-04-15 09:27:08 +02:00