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Copilot chat: multi-agent UI, Plan/Execute questions, progress, cleanup - #1473

Merged

olsonanl merged 157 commits into

BV-BRC:alphafrom

cucinellclark:alpha-hardening

Oct 29, 2026

Merged

Copilot chat: multi-agent UI, Plan/Execute questions, progress, cleanup#1473
olsonanl merged 157 commits into
BV-BRC:alphafrom
cucinellclark:alpha-hardening

Commits on Feb 28, 2026
- stashing
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  committed
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- Merge branch 'copilot-dev' of github.com:cucinellclark/bvbrc_website into copilot-dev
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  committed
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Commits on Mar 4, 2026
- Merge branch 'copilot-dev' of github.com:cucinellclark/bvbrc_website into copilot-dev
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  committed
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Commits on Mar 13, 2026
- stash archaeopteryx
  
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Commits on Apr 9, 2026
- changing grids to use cursor pagination
  
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  authored and
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  committed
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- Merge branch 'BV-BRC:alpha' into alpha
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  authored
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Commits on May 13, 2026
- Merge branch 'copilot-dev' of github.com:cucinellclark/bvbrc_website into copilot-dev
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  committed
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- Merge remote-tracking branch 'origin/alpha' into copilot-dev
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- syncing copilot dev with alpha
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- updating to handle new agent setup
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- removing workflow plan
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Commits on May 15, 2026
- stashing
  
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Commits on May 21, 2026
- Merge branch 'alpha' into copilot-dev
  
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- Merge branch 'copilot-dev' into copilot-dev-agents
  
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  committed
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- updating sse events
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Commits on May 26, 2026
- adding auto submission preferences
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  bf1334f
Commits on May 27, 2026
- hopefully updating th front end to work with the workflow engine better
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  ed72e68
- fixing front end workflow response
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  0eda770
- trying to stop conflicting streams
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  530f6d0
- adding support for text files in chat
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Commits on Jun 5, 2026
- improvements to support multi-agent setup
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  eacf191
Commits on Jun 12, 2026
- Merge remote-tracking branch 'origin/alpha' into copilot-dev-agents
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- Update frontend to use GoWe workflow engine API
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  d60aef1
- Propagate submission_id for GoWe status tracking
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- Merge branch 'copilot-dev-agents' of github.com:cucinellclark/bvbrc_website into copilot-dev-agents
  
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Commits on Jul 17, 2026
- adding workspace object selection widgets
  
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- updates
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- updating
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- updating
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Commits on Jul 18, 2026
- new UI card for answered questions
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- fixing random undefined message
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- fixing more undefined messages
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- get rid of empty message
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- some fixes
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- omit empty assistsant messages
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- more fix attempts
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- another fix
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Commits on Jul 19, 2026
- attempeting interactive genome groups
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- sticker plan tracker
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- fixes
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- bug fixes
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- updating
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  4c9c1d1
- fixes
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  committed
  6210218
- removing plan when switching chats
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  committed
  b197462
- updating
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  committed
  904b70b
- updates to genome group chat UI
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  committed
  43d8684
- more fix attempts
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  committed
  18b3d44
- switching to radio button
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Commits on Jul 20, 2026
- fixes
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- fixes
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  committed
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- changes to support waiting for job completion
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  committed
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- plan card polling
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Commits on Jul 22, 2026
- fixing list link in planning card
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  e0bad41
- fix double slash bug
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  32e8cb9
- fixing url encoding
  
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  committed
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- edit and resubmit
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  committed
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- link fix
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- hopeful fable updates
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Commits on Aug 11, 2026
- fixes for workflows in UI
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Commits on Aug 12, 2026
- changes to planning agent interaction
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- disabling plan tracker
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  3eb39f1
- removing messages and grids chat window tabs
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  a629da6
- turn of edit mode if on and press edit button
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Commits on Aug 14, 2026
- adding go to session folder button
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- creating chats folder
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Commits on Aug 18, 2026
- removing dead coce
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Commits on Aug 19, 2026
- figuring out screenshot issue
  
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  authored and
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  committed
  c7f91ce
- removing lots of unneeded code
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- fixing screenshot
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- stll some issues
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- save to downloads folder for debugging
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- removing save to downloads
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- added an attachments button and have them appear in the chips below the text area
  
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Commits on Aug 20, 2026
- trying to rework chat cards
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- reworking how links and such are generated, downloads
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Commits on Aug 21, 2026
- attempting workflow info rework
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  committed
  16e1bda
- fixing planning bug
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  committed
  c76dfea
- fixing plan card
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  committed
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- removing plan card genome group creation
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- fixing job service name in scroll card job status
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- trying to get better job updates
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Commits on Aug 24, 2026
Commits on Aug 25, 2026
- adding resend button and moving copy button below user message
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- fixing button layout
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- fixing
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- fixing couple more things
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- making refresh arrow lighter
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- changing opacity
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- reworking text input area
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- putting spacing on the input widget
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- increasing padding
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- remove top header report an issue
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- moving edit session button
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- increasing padding for input widget
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- putting border around input area
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- adding shadow to composer
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- slightly stronger shadow
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  committed
  784f677
- fixing ui plan bug
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  committed
  205c5b3
- fixing bugs due to two chat isntances
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- dealing with needs input during plans
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Commits on Aug 26, 2026
- fixing chat session title but
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Commits on Aug 27, 2026
- attempting to fix fasta in text display issue
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Commits on Aug 31, 2026
- trying to enable reconnecting
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  committed
  b24438b
- trhing to make a fix
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  committed
  f73c405
- trying to fix update issue
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- debugging
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- moving rating stars to options, running chip
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- trying to fix running polling
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- removing running chip color flux
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Commits on Sep 2, 2026
- fixing some scroll bar and chat title bugs
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- fixing pdf attachment bug
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  ec83d49
- extending workspace upload to a couple other things
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Commits on Sep 14, 2026
- feat: update queued SSE copy to use gateway message
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  committed
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- fixing chat session title bug
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  6e087c2
- fixing username bug
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  6eb97d1
- Revert "fixing username bug"
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  c728fe6
- Revert "fixing chat session title bug"
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Commits on Sep 17, 2026
- fix: rename .chats to chats in session workspace paths
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Commits on Sep 18, 2026
- planning and execution mode
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- improvements
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Commits on Oct 8, 2026
- fix(copilot): render markdown images in chat replies as links, not <img>
  
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  claude
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- fix(copilot): register a new user's first chat (page-load session)
  
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- fix(copilot): sidebar entry for a restored, never-saved session
  
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Commits on Oct 12, 2026
- feat(copilot): "Submit this job" sends the card's blocked_actions for verbatim replay
  
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- feat(copilot): TURN_IN_FLIGHT returns the message to the input box
  
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- fix(copilot): a finished turn in another chat no longer shows up in the new chat
  
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Commits on Oct 14, 2026
- copilot: prepared-jobs card asks one Yes / No / Other question (D4 Phase 1)
  
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- copilot: plans run in Plan mode; a step pauses on its question (D4 Phase 3)
  
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- copilot: a question card keeps its answer when the chat re-renders
  
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Commits on Oct 15, 2026
- copilot: Stop before the first event stops the turn by session
  
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  committed
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- Merge BV-BRC/BV-BRC-Web alpha (v3.60.5) into alpha-hardening
  
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- copilot: chat titles come from the first user message only
  
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- copilot: plan actions show "Running" in the sidebar
  
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- copilot: jump-to-latest button; "New response" when a reply finishes off-screen
  
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- Copilot UI fixes: delete confirm, cog menu acts on its chat, clarifying questions
  
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Commits on Oct 20, 2026
- copilot: download links in answers fetch every row (cursor paging)
  
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- copilot: questions card for every agent; answers go back to who asked
  
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- copilot: big downloads write to disk as they arrive (Chrome/Edge); dialog wraps
  
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- copilot: download dialog says when the browser holds the file in memory
  
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- copilot: center the jump-to-latest arrow
  
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- copilot: show the Copilot button when logged out, with a log-in prompt
  
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- copilot: job-completed messages appear without a reload
  
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- copilot: execution card knows edit_group ("Update this group?")
  
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- copilot: a job-completed message found by the poll lights "New response"
  
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Commits on Oct 22, 2026
- copilot: live progress as structured steps, four switchable views
  
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- copilot: progress card is collapsed for everyone; no view toggle
  
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Commits on Oct 26, 2026
- Merge upstream/alpha (v3.60.7) into alpha-hardening
  
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- copilot: follow the progress card while a turn runs
  
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- copilot: remove dead tool_call code and the retired CopilotToolHandler
  
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Commits on Oct 27, 2026
Commits on Oct 28, 2026
- config.js: back to the upstream defaults
  
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- Grids: back to upstream offset paging (drop cursor pagination from the PR)
  
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Commits on Oct 29, 2026
- Merge upstream/alpha (v3.60.8) into alpha-hardening
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  committed
  f8de966

Commits

Commits on Feb 28, 2026

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Commits on Aug 27, 2026

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Commits on Sep 2, 2026

Commits on Sep 14, 2026