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

instructions/mcp-read-server.md

@@ -96,7 +96,7 @@ everything an operator needs that is *true of the software* rather than of one i
    stamped `"commit": null`, because a dirty tree corresponds to no revision.
 
    **Never add `git clean` to this sync.** `reset --hard` leaves every gitignored path alone by
-   design, which is exactly what keeps `mcp-upload/` (the `submit` tool's own quarantine) and
+   design, which is exactly what keeps `quarantine/` (the intake channels' quarantine) and
    `reports/telemetry/` intact across a sync - a `git clean -xd` bolted on "to tidy up" would
    delete a submission nobody has reviewed yet, silently, on the next poll.
 
@@ -112,8 +112,8 @@ everything an operator needs that is *true of the software* rather than of one i
 - **Asked to expose a write tool?** Five of the six tools have none, structurally: the server
   imports nothing under `chemenu.commands`, so `new`, `touch`, `xref`, `cite`, `publish` and
   `migrate` are unreachable from it rather than filtered out of a list. The one exception is
-  `submit` (opt-in via the `upload` settings section): it may write, but only into
-  `mcp-upload/`, a quarantine no other command reads - a **positive list** enforced in code
+  `submit` (opt-in via a channel with the handler `mcp` in the `intake` settings section): it may write, but only into
+  `quarantine/`, a quarantine no other command reads - a **positive list** enforced in code
   (`chemenu.upload._write_atomic_within`), not an absence. The commands that move a submission
   *out* of that quarantine (`upload accept`/`upload reject`) still have the absence property:
   they live under `chemenu.commands` and stay unreachable from the server. Reviewing what