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@gordonwoodhull gordonwoodhull commented Nov 20, 2025

replaces #13701

Working branch for CI while I work out dependency and build issues.

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gordonwoodhull and others added 28 commits November 20, 2025 13:31
Begins the major architectural refactoring to enable external execution engines.

Core Architecture:
- Split ExecutionEngine into Discovery/Instance pattern
- Introduce _discovery flag for new pattern
- Create EngineProjectContext as limited ProjectContext subset
- Enable loading engines from external URLs
- Rename LaunchedExecutionEngine → ExecutionEngineInstance

Quarto API Foundation:
- Create @quarto/types package with TypeScript definitions
- Start implementing QuartoAPI interface
- Begin building type system for external engines

Co-Authored-By: Claude <[email protected]>
Ports Julia engine to the new ExecutionEngineDiscovery/Instance pattern
while continuing to build out the Quarto API.

Julia Engine:
- Port julia to ExecutionEngineDiscovery/Instance interfaces
- Explore moving julia out of core (attempted, reverted, restored with override)
- Lay groundwork for julia as bundled extension

Quarto API Expansion:
- Add quarto.jupyter namespace (capabilities, daemon management)
- Add quarto.path.* APIs (resource, runtime, dataDir)
- Add quarto.format utilities and complete Format type
- Add quarto.system APIs for process execution
- Add mapped string utilities
- Bundle types package for distribution
- Pass quarto API to init(), claimsFile, populateCommand
- Rename asLaunchedEngine → asEngineInstance throughout

Co-Authored-By: Claude <[email protected]>
Completes porting of core engines to ExecutionEngineDiscovery pattern
and finishes core Quarto API functionality.

Jupyter Engine Port:
- Port jupyter to ExecutionEngineDiscovery interface (7-part series)
- Update kernel management and cell execution for new pattern
- Fix uses of legacy ExecutionEngine in jupyter code

Knitr Engine Port:
- Port knitr to ExecutionEngineDiscovery interface
- Update R Markdown engine to work with new pattern

API Completion:
- Add system.onCleanup and path.dataDir to API
- Move _discovery flag to engine implementations
- Reorganize types by function for better structure
- Clean up type exports and build configuration
- Remove quarto.markdown, relocate asYamlText and breakQuartoMd
- Port percent.ts to use quarto API
- Use mapped types for FormatIdentifier

Co-Authored-By: Claude <[email protected]>
Completes the architecture migration by cleaning up legacy code and making
the check command extensible for external engines.

Julia as Bundled Extension:
- Use ported julia engine from extension (not core)
- Julia now serves as reference implementation for external engines

Legacy Code Removal:
- Remove legacy ExecutionEngine adapter pattern
- Remove deprecated ExecutionEngine interface and _discovery flags
- Add quartoRequired version checking for execution engines

Check Command Extensibility:
- Make quarto check dynamically extensible via ExecutionEngineDiscovery
- Move check logic into individual engine implementations
- Load external engines in cmd.ts before validation
- Add quarto.system.checkRender() API
- Fix issue where check was discovering CWD as project

API Polish:
- Fix jupyter API message function signatures in quarto-types
- Add console namespace to Quarto API (spinner, output utilities)
- Add inputFilesDir and additional Jupyter methods

Co-Authored-By: Claude <[email protected]>
Implements tooling and infrastructure for managing engine extensions as
git subtrees, enabling them to be maintained in separate repositories
while bundling them with Quarto releases.

Git Subtree Infrastructure:
- Add 'quarto dev-call pull-git-subtree' command to update subtree extensions
  from their source repositories
- Support git subtree directory structure in bundled extensions
- Fix pull-git-subtree to search current branch only with debug logging
- Remove re-authoring logic from pull-git-subtree

Julia Bundled Extension:
- Move julia engine to bundled extensions (first bundled engine)
- Update tests to account for julia-engine bundled subtree extension

Build Fix:
- Fix quarto-bld missing V8 experimental regexp engine flag

Co-Authored-By: Claude <[email protected]>
Final touches to the engine architecture and improvements to Julia
engine testing.

Architecture Polish:
- Fix Windows dynamic import by converting paths to file:// URLs
- Make engineCommand dynamic to support external engines
- Correct relative path handling
- Refactor project initialization and fix julia test cleanup

Julia Testing:
- Refactor julia tests to use proper Deno test steps
- Improve test structure and cleanup

Co-Authored-By: Claude <[email protected]>
Single-file renders now initialize a ProjectContext with config, enabling
both engine and metadata extensions to work without requiring _quarto.yml.

Key changes:
- Single-file ProjectContext now has config = { project: {} } instead of
  undefined, making it consistent with multi-file projects
- Pass full RenderOptions to singleFileProjectContext for extension services
- Export mergeExtensionMetadata() and resolveEngineExtensions() from
  project-context.ts for use in single-file path
- Call both functions in singleFileProjectContext() following same order
  as regular projects
- Use context.dir consistently for extension discovery

Extension output-dir handling:
- When extensions contribute output-dir metadata, set forceClean to match
  the behavior of --output-dir flag, ensuring proper cleanup of the
  temporary .quarto directory (addresses #9745, #13625)
- Warn users when extension contributes output-dir, showing the path and
  whether cleanup will occur (respects --no-clean flag)

Co-Authored-By: Claude <[email protected]>
Completes the external engine ecosystem with user-facing tools and
organizational improvements.

Git Subtree Organization:
- Separate git subtree extensions into extension-subtrees/ directory to
  distinguish from other bundled extensions
- Update subtree extension directory handling and tests
- Remove bundled subtree extensions from input to pandoc to avoid
  duplicate processing

Engine Template:
- Add 'engine' extension template for quarto create
- Include Discovery/Instance pattern boilerplate
- Fix hardcoded "example" references in engine template
- Improve engine template and error handling
- Add cell language prompt for engine configuration
- Add engine extension type to basic creation tests

Metadata Display:
- Filter bundled engines from metadata display output
- Suppress expected/noisy engine metadata while preserving user's custom engines

Co-Authored-By: Claude <[email protected]>
this was a red herring in my investigation, but this is the correct thing to do

will squash into the proper commit later.
that reaches out of quarto-cli
this caused quarto-latexmk not to build correctly
yet another instance of #9737
this was causing dependencies to blow up
where quarto-latexmk was trying to load all execution engines
Implements MVP of `quarto dev-call build-ts-extension` command that:
- Type-checks TypeScript extensions against Quarto API types
- Bundles extensions into single JavaScript files using esbuild
- Provides default configuration for extensions

Key features:
- Auto-detects entry point (config, single file, or mod.ts)
- Config resolution (user deno.json or default from share/extension-build/)
- Type checking with Deno's bundled binary
- Bundling with esbuild's bundled binary
- --check flag for type-check only

Distribution setup:
- Static config templates in src/resources/extension-build/
- Copied to share/extension-build/ during packaging
- Works in both dev mode and distribution mode

Test extension:
- Minimal test in tests/smoke/build-ts-extension/
- Implements ExecutionEngineDiscovery interface
- Demonstrates type-checking and bundling

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>
…odes

Problem: import-map.json pointed to ./quarto-types.d.ts which doesn't
exist in dev mode (src/resources/extension-build/).

Solution: Follow Lua filter transformation pattern:
- Source file in src/resources/ uses dev-mode path
- Transform during packaging for distribution

Changes:
- import-map.json now points to ../../../packages/quarto-types/dist/index.d.ts
  (works in dev mode from src/resources/extension-build/)
- Added updateImportMap() function in prepare-dist.ts that:
  - Runs after supportingFiles() copies all resources
  - Transforms @quarto/types path to ./quarto-types.d.ts for distribution
  - Updates all Deno std versions from src/import_map.json
  - Loops over all imports dynamically (not hardcoded list)
- Updated README.md to document dev vs distribution behavior

Result: Default config now works in dev mode without committing generated
artifacts to src/resources/.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>
Implements --init-config flag that generates a minimal deno.json with
an absolute importMap path pointing to Quarto's bundled configuration.

Features:
- Checks if deno.json already exists and errors with helpful message
- Creates minimal config with compilerOptions and absolute importMap path
- Uses resourcePath() to get correct path in dev and distribution modes
- Exits without building (config generation only)
- Shows helpful customization guidance for users

Example output:
  ✓ Created deno.json
    Import map: /usr/local/share/quarto/extension-build/import-map.json

  Customize as needed:
    - Add "quartoExtension" section for build options
    - Modify "compilerOptions" for type-checking behavior

Generated deno.json points to Quarto's shared import-map.json which
provides @quarto/types and Deno std library imports with correct versions.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>
Remove vendored quarto-types approach and restructure engine template
to match the build-ts-extension specification.

Changes:
- Remove backward compatibility quarto-types copy from prepare-dist.ts
- Remove vendoring logic from artifacts/extension.ts
- Move TypeScript source from _extensions/ to src/ in engine template
- Update _extension.yml to reference .js output instead of .ts
- Update imports to use @quarto/types via import map
- Add build instructions to README
- Fix deno.json to include "deno.ns" in lib array (both default and --init-config)

Engine extensions now follow the spec:
- Source in src/
- Build to _extensions/<name>/<name>.js using build-ts-extension
- Reference types via import map (no vendored copies)

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>
Replace manual directory scanning with expandGlobSync to find _extension.yml
files, properly supporting nested organization structures like
_extensions/org-name/extension/_extension.yml.

Changes:
- Use expandGlobSync("_extensions/**/_extension.yml") pattern
- Support both flat and nested extension directory structures
- Simplify logic by removing manual directory iteration
- Improve error messages with cleaner relative path display

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>
Remove Deno std entries from import map since esbuild cannot bundle
external URL schemes (jsr:, npm:, https:). Add externals support for
marking imports as external (not bundled).

Changes to quarto-cli:
- Simplify import-map.json: only @quarto/types remains
- Simplify updateImportMap(): just path transformation, no version syncing
- Add externals?: string[] to quartoExtension interface
- Implement --external flag handling in bundle function
- Add default externals to deno.json: ["jsr:*", "npm:*", "https:*", "http:*"]

Rationale:
- esbuild binary only bundles relative file paths
- External URL schemes must be resolved at runtime by Deno
- Import map now serves single purpose: @quarto/types aliasing
- Extension authors use full JSR URLs in source code
- Default externals cover all non-bundleable schemes

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>
Switch from esbuild to deno bundle for better import map support and
simpler tooling. deno bundle natively handles JSR/npm/https imports
and does type-checking + bundling in one step.

Changes:
- Replace esbuild with deno bundle in bundle() function
- Remove typeCheck() function (deno bundle does both)
- Restore import map entries for Deno std libraries
- Restore updateImportMap() version syncing in prepare-dist.ts
- Remove externals from quartoExtension interface (not needed)
- Add validateExtensionYml() to warn about path mismatches
- Simplify main action: --check uses deno check, normal build uses deno bundle

Benefits:
- Import maps work natively (no external URL workarounds)
- Extension authors can use bare imports ("path" vs "jsr:@std/[email protected]")
- One tool instead of two (simpler, faster)
- Native support for jsr:, npm:, https: imports
- Version consistency with Quarto maintained via import map
- ~60 lines of code removed

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>
Adds support for specifying the entry point as a command-line argument:
  quarto dev-call build-ts-extension [entry-point]

Entry point resolution priority (highest to lowest):
1. [entry-point] command-line argument
2. quartoExtension.entryPoint in deno.json
3. Single .ts file in src/ directory
4. src/mod.ts if multiple files exist

This allows building extensions with multiple TypeScript files without
requiring a deno.json just to specify the entry point.

Updated error messages to suggest both CLI argument and deno.json options.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>
Renamed the deno.json configuration section from "quartoExtension" to
"bundle" for better semantic alignment with the underlying deno bundle
command.

Mapping to deno bundle CLI options:
- bundle.entryPoint → [file] positional argument
- bundle.outputFile → --output <output> (✅)
- bundle.minify → --minify (✅)
- bundle.sourcemap → --sourcemap[=<sourcemap>] (✅)

The "bundle" name is more intuitive and accurately reflects that these
are bundling configuration options that map to deno bundle CLI flags.

Updated all references:
- Interface definition: DenoConfig.bundle
- All config.bundle references throughout
- Documentation strings
- Error messages with example JSON

Example deno.json:
{
  "bundle": {
    "entryPoint": "src/main.ts",
    "outputFile": "_extensions/my-ext/main.js",
    "minify": true,
    "sourcemap": "linked"
  }
}

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>
Refactored output path resolution to support three modes:

1. Just filename (no path separators):
   { "bundle": { "outputFile": "julia-engine.js" } }
   → Infers directory from _extension.yml location
   → Result: _extensions/julia-engine/julia-engine.js

2. Full path (has path separators):
   { "bundle": { "outputFile": "_extensions/custom/out.js" } }
   → Uses path as-is
   → Result: _extensions/custom/out.js

3. Omitted:
   { "bundle": {} }
   → Infers both filename (from entry point) and directory
   → Result: _extensions/julia-engine/julia-engine.js

Implementation changes:
- Split into two focused functions:
  - inferFilename(entryPoint): derives "foo.js" from "src/foo.ts"
  - inferOutputPath(outputFilename): finds _extension.yml and joins with filename
- Updated bundle() to detect filename-only vs full-path
- Each function has single responsibility, no coupling

This provides flexibility while maintaining convention over configuration.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>
…m commit 2fb2adf6e

git-subtree-dir: src/resources/extension-subtrees/julia-engine
git-subtree-split: 2fb2adf6ef7b24272ff76a54ee0b51b5f6962a66
@gordonwoodhull gordonwoodhull force-pushed the feature/engine-extension-3 branch from ecb4468 to 9aedc82 Compare November 20, 2025 18:32
gordonwoodhull and others added 16 commits November 20, 2025 13:41
Moves the build-ts-extension command from the hidden dev-call namespace
to the public call command namespace, making it accessible to users.

Changes:
- Moved src/command/dev-call/build-ts-extension/ to src/command/call/build-ts-extension/
- Removed .hidden() flag from command definition
- Updated error messages to reference 'quarto call build-ts-extension'
- Added command registration to src/command/call/cmd.ts
- Removed command registration from src/command/dev-call/cmd.ts

The command is now available as:
  quarto call build-ts-extension [entry-point]

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>
…m 2fb2adf6e..db03cb0c5

db03cb0c5 add checkInstallation stub

git-subtree-dir: src/resources/extension-subtrees/julia-engine
git-subtree-split: db03cb0c58661064db5bd6c1c083b828c8276749
…e context

Fixes the issue where `quarto check julia` was failing with "Invalid value 'julia'"
even though Julia is available as a bundled engine extension.

The problem: When running commands like `quarto check julia` outside a project
directory, no project context exists, so bundled engine extensions were never loaded.

The solution: Create a zeroFileProjectContext() that provides just enough structure
to discover and register bundled engine extensions when no actual project or file
exists. The function initializeProjectContextAndEngines() now falls back to this
zero-file context when no project is found.

Also changed initializeProjectContextAndEngines() to return Promise<void> instead
of Promise<ProjectContext | undefined>, since the name suggests initialization
rather than retrieval and both callers ignore the return value.

Now `quarto check julia` works both inside and outside project directories.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>
Make error messages more helpful by:
- Only showing deno.json configuration when deno.json already exists
- This discourages users from creating deno.json when they don't need it
- Use relative paths in examples instead of absolute paths
- Order solutions from simplest to most complex (CLI arg, then rename, then config)

Changes:
- "No src/ directory" error: Show CLI argument first, only show deno.json config if it exists
- "Multiple .ts files" error: Show CLI argument first, then rename to mod.ts, then deno.json (if exists)
- "Multiple extensions" error: If no deno.json, explain this isn't supported and suggest --init-config; if deno.json exists, show how to configure outputFile
- Use relative paths in outputFile example (strip absolute path prefix)

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>
- llm-docs/quarto-api.md: Step-by-step guide for adding functionality to
  the Quarto API (type definitions in @quarto/types and implementation in
  quarto-api.ts), including usage patterns for internal and external engines
- llm-docs/error-messages.md: Style guide for writing idiomatic error
  messages with proper newline placement (end messages with \n, never start
  with \n or use empty calls)
Engine extensions now require quarto call build-ts-extension to bundle
TypeScript before rendering. Updated test to build before attempting to
render the created extension.
When a test fails on Windows, exit immediately instead of continuing through
remaining tests in the bucket. This matches Linux behavior (bash -e flag) and
keeps test failures at the end of the log where they're easy to find, instead
of buried under 1000+ lines of subsequent test output.
also, load builtin engine extensions
…m db03cb0c5..7eaf7bc3d

7eaf7bc3d claude: use quarto api for logging

git-subtree-dir: src/resources/extension-subtrees/julia-engine
git-subtree-split: 7eaf7bc3d77aa439805baa9d59df96633825fa48
…m 7eaf7bc3d..9bb6ee655

9bb6ee655 artifact

git-subtree-dir: src/resources/extension-subtrees/julia-engine
git-subtree-split: 9bb6ee655388780db187cb48bdd8e34aed89148d
…prove error messages

Check configEntryPoint before validating src/ directory existence, allowing non-extension projects to specify custom entry points. Clarify error message when outputFile lacks a path by suggesting ./ prefix as an alternative to creating _extensions structure.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>
Add test that verifies build-ts-extension correctly bundles TypeScript engine extensions. Test validates that imports from the import map (like @std/path) are properly bundled into the output JavaScript file.

Remove deno.json from test to verify auto-detection of entry point from src/ directory works correctly.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>
Wrap log.info/warning/error in arrow functions instead of direct references in quartoAPI object. This prevents the bundler from creating top-level async initialization code.

When functions are assigned directly at module level (e.g., `{ info, error }`), the bundler assumes they might be accessed immediately and inserts top-level await calls to initialize underlying Deno extensions. Wrapping them in arrow functions defers access until the functions are actually called, avoiding the top-level await issue.

Fixes prepare-dist workflow error:
  await init_quarto_api();
  ^
  SyntaxError: Unexpected reserved word

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>
@gordonwoodhull
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gordonwoodhull commented Nov 22, 2025

I think this PR has passed through bundler hell and could be ready to merge.

It required some dynamic imports due to new dependencies from check and command to render modules using module level await, triggering esbuild bundler bugs in test-bundle

Then those fixes caused spurious eslint variables not found, disabled in validate-bundle.

So, yeah! I’m not excited about merging it with problems I fundamentally don’t understand. I’m going to sleep on it.

gordonwoodhull and others added 5 commits November 26, 2025 04:03
Add a --dev flag to `quarto run` that uses the main development import map
(src/import_map.json) instead of the user-facing run_import_map.json. This
allows internal development tools (like import-report scripts) to access
the full quarto development environment including deno_ral and other
internal modules.

Not visible for end users; description is for documentation purposes only.

Usage:
  quarto run --dev script.ts [args...]

The --dev flag should be used for internal quarto development tools that
import from src/deno_ral or src/core. User-facing scripts should continue
to use the standard `quarto run` without --dev.

Co-Authored-By: Claude <[email protected]>
…ules

If you have a dependency cycle where all of the modules are async
(transitively because of their dependencies) then it would probably
deadlock if you ran it.

esbuild gives up and emits invalid JS.

So you must either break these cycles, or prevent the async from
propagating to the cycles.

This tool uses ILP to show
- Minimal places to break remove static imports to stop transitive
dependencies before they hit cycles (minimal hitting set)
- Minimal places to remove static imports to break these cycles
(minimum feedback arc set)

Co-Authored-By: Claude <[email protected]>
Fix async bundler issues by combining MFAS-recommended dynamic imports
with architectural refactoring to eliminate circular dependency.

## Changes

### 1. Dynamic Import Fixes (MFAS recommendations)

Added dynamic imports to break async propagation through cycles:

- src/command/check/check-render.ts
  * Made render-shared.ts import dynamic in checkRender()
  * Prevents async from propagating into render modules

### 2. Architectural Refactoring

Eliminated circular dependency between engine.ts and command-utils.ts:

**Created:** src/command/call/engine-cmd.ts
- Moved engineCommand definition from engine.ts
- Imports core functions: executionEngine(), executionEngines()
- Imports initializeProjectContextAndEngines from command-utils.ts
- Follows existing command pattern (check/cmd.ts, render/cmd.ts)

**Modified:** src/execute/engine.ts
- Removed engineCommand export (40 lines)
- Removed import of initializeProjectContextAndEngines
- Now contains only core engine logic

**Modified:** src/command/call/cmd.ts
- Updated import to use new ./engine-cmd.ts

**Modified:** src/command/command-utils.ts
- Removed dynamic import workaround for reorderEngines
- Restored clean static import from engine.ts

## Impact

The 2-cycle between engine.ts ↔ command-utils.ts is eliminated:
- engine.ts no longer imports from command-utils.ts
- command-utils.ts cleanly imports from engine.ts
- engineCommand now lives in proper command file

## Result

- Eliminates circular dependency completely
- Only 2 dynamic imports remain (essential async propagation fixes)
- Better architecture: CLI separated from core engine logic
- Follows existing codebase patterns
- Build succeeds without async bundling errors
- Net reduction: 38 lines of code

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>
Breaks the async propagation chain from hash.ts by converting the static
import of withCriClient to a dynamic import. This prevents esbuild from
marking core/handlers/base.ts as async, which was causing it to propagate
async to 14 cyclic files, generating invalid bundle code.

The ILP optimizer identified this single import as the optimal break point
affecting all 14 async propagation chains.

Changes:
- Remove static import of withCriClient from core/cri/cri.ts
- Add getCriClient() helper function with dynamic import
- Update extractHtml() to use getCriClient()
- Update createPngsFromHtml() to use getCriClient()

Result: Bundle builds successfully with no async cycle errors.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>
Move executeResultIncludes and executeResultEngineDependencies from
src/execute/jupyter/jupyter.ts to src/core/jupyter/jupyter.ts.

These functions are shared utilities used by multiple engines, not
engine-specific logic. Moving them to core breaks a circular dependency:
- src/core/quarto-api.ts was importing from src/execute/jupyter/jupyter.ts
- src/execute/jupyter/jupyter.ts was importing quartoAPI
- This created a cycle: core → execute → core

With this change, the dependency flow is now one-way:
- Engines (execute/) import from quartoAPI (core/)
- quartoAPI imports from core utilities (core/jupyter/)
- Core utilities have no dependency on engines

This is a prerequisite for implementing true dependency inversion via
the registry pattern, which will eliminate remaining circular dependencies.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude <[email protected]>
@gordonwoodhull gordonwoodhull force-pushed the feature/engine-extension-3 branch from 14c5b2d to 0e273bd Compare November 27, 2025 01:53
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3 participants