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/explanation/architecture.md

@@ -81,9 +81,10 @@ chemenu/
 │   ├── ingest-large-tree.md
 │   ├── ingest-queue.md # Reviewing a submission before wikitool upload accept promotes it
 │   └── wiki-*/SKILL.md # Skills - copied into .agents/skills/ and .claude/skills/
-├── mcp-upload/         # QUARANTINE (optional): the MCP `submit` tool's write path, gitignored -
-│                       #   read by no command in the ordinary pipeline; a human reviews it with
-│                       #   `wikitool upload list/show/accept/reject`
+├── quarantine/         # QUARANTINE (optional): where the intake channels (MCP `submit`, a synced
+│                       #   folder, a command) put what nobody has reviewed, gitignored - read by
+│                       #   no command in the ordinary pipeline; a human reviews it with
+│                       #   `wikitool upload list/show/accept/reject`, `upload collect` fills it
 ├── incoming/           # INBOX: content gitignored - drop a file or one folder per source here, `raw accept` promotes it
 ├── raw/                # INPUT: immutable, untrusted source material
 │   ├── CONTRACT.md     # Date shard, capture fields, immutability, untrusted content

docs/explanation/pipeline-rationale.md

@@ -19,9 +19,11 @@ not yet reviewed and not yet a citation target, so its being gitignored and read
 ingest session does not weaken anything - the boundary is the promotion into `raw/` itself, not
 the moment a human happened to drop a file somewhere.
 
-Once a document can arrive from *outside* - the MCP server's optional `submit` tool - "a human
-happened to drop a file somewhere" stops describing how everything reaches `incoming/`, so the
-near side of the boundary gets a stage of its own rather than a second meaning. `mcp-upload/`
+Once a document can arrive from *outside* - the MCP server's optional `submit` tool, a folder a
+sync client fills, a program of the checkout - "a human happened to drop a file somewhere" stops
+describing how everything reaches `incoming/`, so the near side of the boundary gets a stage of its
+own rather than a second meaning. Every such channel ends in the same `quarantine/`, because what
+the boundary protects against is the lack of a reviewer, not the transport. `quarantine/`
 holds what nobody has looked at yet; `incoming/` holds what someone has. Two arrows, two
 different things being granted: `upload accept` grants *trust* (a human read the material and
 took responsibility for it), `raw accept` grants *immutability* (it becomes a citation target