intake: several configured intake channels (mcp, folder, command) all end in quarantine/ (was mcp-upload/), and upload collect pulls the synced-folder and command channels into it (#213); 10.0.0-beta.11

Files changed:
- .gitignore
- CHANGES.md
- VERSION
- docs/explanation/architecture.md
- docs/explanation/pipeline-rationale.md
- docs/how-to/README.md
- docs/how-to/back-up-to-a-synced-folder.md
- docs/how-to/collect-from-a-synced-folder.md
- docs/how-to/ingest-a-source.md
- docs/how-to/set-up-the-mcp-server.md
- docs/reference/commands/README.md
- docs/reference/commands/git.md
- docs/reference/commands/instance-health.md
- docs/reference/commands/raw-material-and-uploads.md
- docs/reference/configuration.md
- instructions/gates.md
- instructions/ingest-queue.md
- instructions/mcp-read-server.md
- instructions/migrations/10.0.0-settings-tiers.md
- instructions/wiki-ingest/SKILL.md
- raw/CONTRACT.md
- tools/CONTRACT.md
- tools/README.md
- tools/chemenu/cli_contract.py
- tools/chemenu/collect.py
- tools/chemenu/commands/backup_cmd.py
- tools/chemenu/commands/docs_verify.py
- tools/chemenu/commands/doctor.py
- tools/chemenu/commands/raw/pending.py
- tools/chemenu/commands/upload_cmd.py
- tools/chemenu/config.py
- tools/chemenu/config_shapes.py
- tools/chemenu/legacy_settings.py
- tools/chemenu/mcp/server.py
- tools/chemenu/reference_doc.py
- tools/chemenu/tests/test_backup.py
- tools/chemenu/tests/test_collect.py
- tools/chemenu/tests/test_config_shapes.py
- tools/chemenu/tests/test_doctor.py
- tools/chemenu/tests/test_legacy_settings.py
- tools/chemenu/tests/test_mcp_server.py
- tools/chemenu/tests/test_upload.py
- tools/chemenu/tests/test_upload_cmd.py
- tools/chemenu/upload.py

Co-Authored-By: Claude Code <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01SnAJ7Z3CpVD3PRbN73QtU2

docs/reference/commands/README.md

@@ -86,7 +86,8 @@ Full records: [raw-material-and-uploads.md](raw-material-and-uploads.md)
 - [`raw status`](raw-material-and-uploads.md#raw-status) - Report which captured bundles under `raw/` have fallen behind their repository, with each changed file as `A`/`M`/`D`.
 - [`raw pending`](raw-material-and-uploads.md#raw-pending) - List what waits in `incoming/`, oldest first, and name the entry an ingest without an argument takes next.
 - [`raw accept`](raw-material-and-uploads.md#raw-accept) - Promote one or more files, or one folder, from `incoming/` into `raw/`.
-- [`upload list`](raw-material-and-uploads.md#upload-list) - List every MCP submission currently waiting in the quarantine (`mcp-upload/`).
+- [`upload collect`](raw-material-and-uploads.md#upload-collect) - Pull material from the configured `folder` and `command` intake channels into the quarantine - never past it.
+- [`upload list`](raw-material-and-uploads.md#upload-list) - List every submission currently waiting in the quarantine (`quarantine/`), whatever channel it came through.
 - [`upload show`](raw-material-and-uploads.md#upload-show) - Print one submission's manifest in full.
 - [`upload accept`](raw-material-and-uploads.md#upload-accept) - **Upload Review Gate:** promote a submission's file from quarantine into `incoming/`.
 - [`upload reject`](raw-material-and-uploads.md#upload-reject) - Delete a submission's material, keeping only its ledger trail.