Merge origin/main (v1.2.0: Projects, modules, in-app updates)

Reconciles 17 commits of this session's work (self-alteration tools,
vendored Curry, slash-command dispatch, Windows toolchain/gate fixes)
against origin/main's v1.2.0 sync (Projects/RAG scoping, a new modules/
system for mail and network, in-app updates, the standalone memory
microservice folded into an in-process curator, KDE desktop theme
overhaul). Nine real conflicts, each resolved by hand after reading both
sides' actual diffs rather than picking one side wholesale:

- synapse/tools.py, tests/test_tools.py: origin/main's diff here was
  small and clean (read_file/list_files, two new tests) despite git's
  diff3 flagging the whole file as one conflict blob -- reset to this
  branch's version and hand-spliced their addition in at the same
  points they used, rather than trying to reconcile a false 800-line
  conflict. Found and fixed a real bug while verifying: _list_files
  returned backslash-separated paths on Windows, which don't match the
  forward-slash glob patterns the tool's own schema documents.
- synapse/main.py: kept this branch's cue-based standing advertisement
  of render_preview/run_snippet (independent of any playbook granting
  them) AND adopted origin/main's fix for routed reference playbooks
  not bringing their own tools along -- dropping either would have been
  a real regression, not just a style difference. Also: the standalone
  memory service (port 8001) is gone upstream, so its dead CORS/kill-
  target entries were removed; NEXUS_BACKEND_PORT parameterization and
  the manage_ollama-conditional kill logic (this branch's remote-Ollama
  support) were kept over origin/main's hardcoded equivalents.
- synapse/memory/store.py: kept this branch's _delete_message_vectors
  helper (already reused elsewhere, batches to stay under SQLite's
  variable limit) over origin/main's inline duplicate of the same fix.
- synapse/nexus_config.py, nexusos_cli/ncp.py: dropped the now-dead
  memory-service port/service entries; kept NEXUS_BACKEND_PORT env
  override and the manage_ollama-conditional kill-target list.
- CLAUDE.md, README.md: merged both sides' additions, no real conflict.

Found and fixed three more issues while independently verifying the
merged tree, none of them mine or origin/main's alone -- only visible
once both sides actually ran together:

- modules/ (the new mail+network package) was never added to
  pyproject.toml's wheel `packages` list OR the sdist's `include`
  allowlist, so `from modules.registry import ROUTERS` in main.py would
  ImportError on any wheel install. Fixed both; bin/check.sh's
  packaging gate now asserts modules/ actually ships. tests/
  test_packaging_deps.py's FIRST_PARTY/SHIPPED_PACKAGES sets were
  updated to recognize the new package.
- tests/test_mail_creds.py's 0600-mode assertions are POSIX-only --
  NTFS has no equivalent permission bits, so os.open(path, 0o600) on
  Windows just creates a normal file and stat.S_IMODE reports 0o666
  regardless. Made the assertions platform-aware rather than skip real
  coverage (the temp-file-cleanup and password round-trip checks in the
  same test still run on Windows) or paper over a genuine OS
  limitation with a fake pass.
- tests/test_kde_theme.py used bare Path.read_text() in fifteen places;
  Windows' default locale encoding (cp1252, not UTF-8) can't decode a
  real UTF-8 byte in the QML it reads, and did fail on one of the
  fifteen. Fixed all fifteen, not just the one that happened to trip
  today, since the other fourteen were equally fragile.

Verified: full bin/check.sh reports OK end-to-end on this Windows
checkout -- pytest (tests + management): 295 passed, 0 failed, 9
skipped; eslint clean; frontend node:test 57/57; PowerShell/shell
parse clean; wheel + sdist pass twine check and now correctly carry
modules/ (60 files, up from 52 pre-merge). synapse.main:app builds
with 74 routes (up from 54 pre-merge, matching the new Projects/mail/
network endpoints).

tests/test_documents.py

@@ -68,6 +68,45 @@ def test_conversation_project_binding():
     assert s.conversation_project("c2") == ""           # unscoped
 
 
+def test_conversations_move_between_projects():
+    # The Projects page lists chats by project_id and moves them with a PATCH;
+    # if all_conversations() drops the column the list is silently empty.
+    s = _store()
+    s.create_conversation("c1", "projX")
+    s.create_conversation("c2")
+    assert {c.id: c.project_id for c in s.all_conversations()} == {"c1": "projX", "c2": ""}
+
+    s.set_conversation_project("c2", "projX")
+    s.set_conversation_project("c1", "")               # removed from the project
+    assert {c.id: c.project_id for c in s.all_conversations()} == {"c1": "", "c2": "projX"}
+
+
+def test_project_instructions_and_scoped_memory():
+    # The chat system prompt takes the project's instructions plus global facts
+    # and this project's facts only — another project's must never leak in.
+    from synapse.memory.store import MemoryItem
+
+    s = _store()
+    p = s.create_project("Roof rebuild")
+    assert s.project_instructions(p["id"]) == ""        # default: no instructions
+    assert s.project_instructions("ghost") == ""        # unknown project
+    assert s.set_project_instructions(p["id"], "answer as a roofer")
+    assert not s.set_project_instructions("ghost", "x")
+    assert s.project_instructions(p["id"]) == "answer as a roofer"
+
+    s.add(MemoryItem(id="g", text="lives in Ohio"))                          # global
+    s.add(MemoryItem(id="a", text="uses metal panels", project_id=p["id"]))  # this project
+    s.add(MemoryItem(id="b", text="prefers Lua", project_id="other"))        # elsewhere
+    in_scope = [m.id for m in s.all() if m.project_id in ("", p["id"])]
+    assert in_scope == ["g", "a"]
+
+    # Deleting a project keeps its chats and facts, unscoped.
+    s.create_conversation("c1", p["id"])
+    s.delete_project(p["id"])
+    assert s.conversation_project("c1") == ""
+    assert s.get("a").project_id == ""
+
+
 def test_conversation_recall_uses_vec_and_matches_brute_force():
     s = _store()
     if not s.vec_enabled:
@@ -233,3 +272,64 @@ def test_extract_text_by_type():
     out = _extract_text("blank.pdf", buf.getvalue())
     assert isinstance(out, str)  # blank page -> "" or whitespace, never raises
     assert PdfReader(io.BytesIO(buf.getvalue())).pages  # sanity: it was a valid PDF
+
+
+def test_delete_conversation_takes_its_embeddings_with_it(tmp_path, monkeypatch):
+    """Stale vectors are inert — the search joins messages — but they still
+    occupy slots in the ANN over-fetch, so recall of the surviving
+    conversations quietly thins out as deleted ones pile up."""
+    import sqlite3
+    from synapse.memory.store import PersistentMemoryStore
+
+    db = tmp_path / "t.db"
+    s = PersistentMemoryStore(db)
+    s.create_conversation("keep", "")
+    s.create_conversation("drop", "")
+    kept = s.add_message("keep", "user", "hello")
+    doomed = s.add_message("drop", "user", "goodbye")
+
+    conn = sqlite3.connect(db)
+    for mid in (kept, doomed):
+        conn.execute(
+            "INSERT OR REPLACE INTO message_vectors (message_id, embedding) VALUES (?, ?)",
+            (mid, "[0.0, 1.0]"),
+        )
+    conn.commit()
+
+    s.delete_conversation("drop")
+
+    left = {r[0] for r in conn.execute("SELECT message_id FROM message_vectors")}
+    assert left == {kept}, left
+
+
+def test_extraction_watermark_is_idempotent(tmp_path):
+    """The curator reads a conversation when it goes idle, so the watermark is
+    what stops a restart (or a second sweep) from re-reading messages and
+    re-saving the facts it already saved."""
+    from synapse.memory.store import PersistentMemoryStore
+
+    s = PersistentMemoryStore(tmp_path / "t.db")
+    s.create_conversation("c", "")
+    s.add_message("c", "user", "i bought a bike")
+    last = s.add_message("c", "assistant", "nice")
+
+    pending, mark = s.pending_extraction("c")
+    assert [m["role"] for m in pending] == ["user", "assistant"]
+    assert mark == last
+
+    s.set_extracted_through("c", mark)
+    assert s.pending_extraction("c") == ([], 0)     # nothing new -> no model call
+
+    s.add_message("c", "user", "a 2019 trek")
+    pending, _ = s.pending_extraction("c")
+    assert [m["content"] for m in pending] == ["a 2019 trek"]   # only the unread tail
+
+
+def test_idle_sweep_only_claims_quiet_conversations(tmp_path):
+    from synapse.memory.store import PersistentMemoryStore
+
+    s = PersistentMemoryStore(tmp_path / "t.db")
+    s.create_conversation("fresh", "")
+    s.add_message("fresh", "user", "still typing")
+    assert s.conversations_awaiting_extraction(3600) == []   # too recent to be "over"
+    assert s.conversations_awaiting_extraction(0) == ["fresh"]