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/how-to/set-up-the-mcp-server.md

@@ -160,18 +160,19 @@ reviewed yet.
 
 ## Optional: the submit path
 
-Without this, `submit` does not exist as a tool - not unused, but not registered. An
-`upload` section in the served checkout's `.wikitool-local.json` turns it on. Its fields, defaults and what a malformed
-section does are in the [configuration reference](../reference/configuration.md#mcp-submissions); a
-broken section never means "no limits", it stops the server from starting.
+Without this, `submit` does not exist as a tool - not unused, but not registered. A
+channel with the handler `mcp` in the `intake` section of the served checkout's
+`.wikitool-local.json` turns it on. Its fields, defaults and what a malformed section does are in
+the [configuration reference](../reference/configuration.md#intake-channels); a broken section never
+means "no limits", it stops the server from starting.
 
 **With `submit` on, the middleware has a second duty.** It has to set the identity header itself, on
 every authenticated request, and discard any copy the client sent. The server trusts that header as
 the value for `submitter`. A header the client could set itself would be a claim, not an identity.
-If `identity_header` names a header the middleware does not set, every submission is refused for
+If the channel's `identity_header` names a header the middleware does not set, every submission is refused for
 lack of an identity.
 
-Submitted files land in `mcp-upload/<id>/`, which is gitignored and read by no other command. From
+Submitted files land in `quarantine/<id>/`, which is gitignored and read by no other command. From
 there a human promotes or rejects them, in the same checkout as the server rather than in its
 process. That review is part of
 [ingesting a source](ingest-a-source.md#a-document-submitted-from-outside).
@@ -228,7 +229,7 @@ the client starts a different Python than the instance's. Give the client the ab
 
 **`"commit": null` in every answer**: the served tree has uncommitted changes. Either the sync is not
 running, or something writes into the corpus that has no business there. The five read tools never
-write. `submit`, when it is on, writes only to `mcp-upload/`, which is gitignored and so is never a
+write. `submit`, when it is on, writes only to `quarantine/`, which is gitignored and so is never a
 cause of `"commit": null` either.
 
 **`commit` names an old revision**: the sync timer is not running.
@@ -246,6 +247,6 @@ Deployment specifics - the cluster, ingress hosts, the secret store, the GitOps
 private infrastructure, and this repository is public.
 
 There is no container image for the server yet. Until there is, the path above - the venv,
-`python -m chemenu.mcp`, a proxy in front - is the complete one. With `submit` on, `mcp-upload/`
+`python -m chemenu.mcp`, a proxy in front - is the complete one. With `submit` on, `quarantine/`
 has to survive restarts the same way the rest of the checkout does. Otherwise a submitted file that
 nobody has reviewed yet loses its quarantine.