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

.gitignore

@@ -180,18 +180,17 @@ npm-debug.log*
 /incoming/*
 !/incoming/.gitkeep
 
-# MCP `submit` tool quarantine (see raw/CONTRACT.md "Getting a file in from
-# outside" and tools/chemenu/upload.py). Material pushed by a caller that is
-# not this terminal, before a human has reviewed any of it - stronger than
-# `incoming/` above: not merely uncommitted, but read by no command in the
+# The quarantine of the intake channels (see raw/CONTRACT.md "Getting a file in
+# from outside" and tools/chemenu/upload.py). Material that came from a caller
+# that is not this terminal - the MCP `submit` tool, a synced folder, a program
+# of this checkout - before a human has reviewed any of it: stronger than
+# `incoming/` above, not merely uncommitted but read by no command in the
 # ordinary pipeline. Unlike `incoming/` above (Gitea #88), this one keeps the
-# directory form and gets no `.gitkeep`: the directory is created on demand
-# by the one function that is allowed to write into it, and a checkout that
-# never arms the `submit` tool never gets one - there is no fresh-clone case
-# to cover here, since nothing reads this path before that function creates
-# it. Never anchored back open by the content backstop below, same as
-# `incoming/`.
-/mcp-upload/
+# directory form and gets no `.gitkeep`: the directory is created on demand by
+# the one function that is allowed to write into it, together with its own
+# `.gitignore`, so a checkout that never arms a channel never gets one. Never
+# anchored back open by the content backstop below, same as `incoming/`.
+/quarantine/
 
 # Content backstop - keep this block last. Nothing under raw/, kb/, work/ or sites/ may
 # be excluded by a pattern above; see the header note for why directory patterns