fix: schema init ordering, deploy.sh default, client BASE_URL docs

Three issues Dalidou Claude surfaced during the first real deploy
of commit e877e5b to the live service (report from 2026-04-08).
Bug 1 was the critical one — a schema init ordering bug that would
have bitten every future upgrade from a pre-Phase-9 schema — and
the other two were usability traps around hostname resolution.

Bug 1 (CRITICAL): schema init ordering
--------------------------------------
src/atocore/models/database.py

SCHEMA_SQL contained CREATE INDEX statements that referenced
columns added later by _apply_migrations():

    CREATE INDEX IF NOT EXISTS idx_memories_project ON memories(project);
    CREATE INDEX IF NOT EXISTS idx_interactions_project_name ON interactions(project);
    CREATE INDEX IF NOT EXISTS idx_interactions_session ON interactions(session_id);

On a FRESH install, CREATE TABLE IF NOT EXISTS creates the tables
with the Phase 9 shape (columns present), so the CREATE INDEX runs
cleanly and _apply_migrations is effectively a no-op.

On an UPGRADE from a pre-Phase-9 schema, CREATE TABLE IF NOT EXISTS
is a no-op (the tables already exist in the old shape), the columns
are NOT added yet, and the CREATE INDEX fails with
"OperationalError: no such column: project" before
_apply_migrations gets a chance to add the columns.

Dalidou Claude hit this exactly when redeploying from 0.1.0 to
0.2.0 — had to manually ALTER TABLE to add the Phase 9 columns
before the container could start.

The fix is to remove the Phase 9-column indexes from SCHEMA_SQL.
They already exist in _apply_migrations() AFTER the corresponding
ALTER TABLE, so they still get created on both fresh and upgrade
paths — just after the columns exist, not before.

Indexes still in SCHEMA_SQL (all safe — reference columns that
have existed since the first release):
- idx_chunks_document on source_chunks(document_id)
- idx_memories_type on memories(memory_type)
- idx_memories_status on memories(status)
- idx_interactions_project on interactions(project_id)

Indexes moved to _apply_migrations (already there — just no longer
duplicated in SCHEMA_SQL):
- idx_memories_project on memories(project)
- idx_interactions_project_name on interactions(project)
- idx_interactions_session on interactions(session_id)
- idx_interactions_created_at on interactions(created_at)

Regression test: tests/test_database.py
---------------------------------------
New test_init_db_upgrades_pre_phase9_schema_without_failing:

- Seeds the DB with the exact pre-Phase-9 shape (no project /
  last_referenced_at / reference_count on memories; no project /
  client / session_id / response / memories_used / chunks_used on
  interactions)
- Calls init_db() — which used to raise OperationalError before
  the fix
- Verifies all Phase 9 columns are present after the call
- Verifies the migration indexes exist

Before the fix this test would have failed with
"OperationalError: no such column: project" on the init_db call.
After the fix it passes. This locks the invariant "init_db is
safe on any legacy schema shape" so the bug can't silently come
back.

Full suite: 216 passing (was 215), 1 warning. The +1 is the new
regression test.

Bug 3 (usability): deploy.sh DNS default
----------------------------------------
deploy/dalidou/deploy.sh

ATOCORE_GIT_REMOTE defaulted to http://dalidou:3000/Antoine/ATOCore.git
which requires the "dalidou" hostname to resolve. On the Dalidou
host itself it didn't (no /etc/hosts entry for localhost alias),
so deploy.sh had to be run with the IP as a manual workaround.

Fix: default ATOCORE_GIT_REMOTE to http://127.0.0.1:3000/Antoine/ATOCore.git.
Loopback always works on the host running the script. Callers
from a remote host (e.g. running deploy.sh from a laptop against
the Dalidou LAN) set ATOCORE_GIT_REMOTE explicitly. The script
header's Environment Variables section documents this with an
explicit reference to the 2026-04-08 Dalidou deploy report so the
rationale isn't lost.

docs/dalidou-deployment.md gets a new "Troubleshooting hostname
resolution" subsection and a new example invocation showing how
to deploy from a remote host with an explicit ATOCORE_GIT_REMOTE
override.

Bug 2 (usability): atocore_client.py ATOCORE_BASE_URL documentation
-------------------------------------------------------------------
scripts/atocore_client.py

Same class of issue as bug 3. BASE_URL defaults to
http://dalidou:8100 which resolves fine from a remote caller
(laptop, T420/OpenClaw over Tailscale) but NOT from the Dalidou
host itself or from inside the atocore container. Dalidou Claude
saw the CLI return
{"status": "unavailable", "fail_open": true}
while direct curl to http://127.0.0.1:8100 worked.

The fix here is NOT to change the default (remote callers are
the common case and would break) but to DOCUMENT the override
clearly so the next operator knows what's happening:

- The script module docstring grew a new "Environment variables"
  section covering ATOCORE_BASE_URL, ATOCORE_TIMEOUT_SECONDS,
  ATOCORE_REFRESH_TIMEOUT_SECONDS, and ATOCORE_FAIL_OPEN, with
  the explicit override example for on-host/in-container use
- It calls out the exact symptom (fail-open envelope when the
  base URL doesn't resolve) so the diagnosis is obvious from
  the error alone
- docs/dalidou-deployment.md troubleshooting section mirrors
  this guidance so there's one place to look regardless of
  whether the operator starts with the client help or the
  deploy doc

What this commit does NOT do
----------------------------
- Does NOT change the default ATOCORE_BASE_URL. Doing that would
  break the T420 OpenClaw helper and every remote caller who
  currently relies on the hostname. Documentation is the right
  fix for this case.
- Does NOT fix /etc/hosts on Dalidou. That's a host-level
  configuration issue that the user can fix if they prefer
  having the hostname resolve; the deploy.sh fix makes it
  unnecessary regardless.
- Does NOT re-run the validation on Dalidou. The next step is
  for the live service to pull this commit via deploy.sh (which
  should now work without the IP workaround) and re-run the
  Phase 9 loop test to confirm nothing regressed.

scripts/atocore_client.py

@@ -1,8 +1,43 @@
 """Operator-facing API client for live AtoCore instances.
 
-This script is intentionally external to the app runtime. It is for admins and
-operators who want a convenient way to inspect live project state, refresh
-projects, audit retrieval quality, and manage trusted project-state entries.
+This script is intentionally external to the app runtime. It is for admins
+and operators who want a convenient way to inspect live project state,
+refresh projects, audit retrieval quality, manage trusted project-state
+entries, and drive the Phase 9 reflection loop (capture, extract, queue,
+promote, reject).
+
+Environment variables
+---------------------
+
+ATOCORE_BASE_URL
+    Base URL of the AtoCore service (default: ``http://dalidou:8100``).
+
+    When running ON the Dalidou host itself or INSIDE the Dalidou
+    container, override this with loopback or the real IP::
+
+        ATOCORE_BASE_URL=http://127.0.0.1:8100 \\
+            python scripts/atocore_client.py health
+
+    The default hostname "dalidou" is meant for cases where the
+    caller is a remote machine (laptop, T420/OpenClaw, etc.) with
+    "dalidou" in its /etc/hosts or resolvable via Tailscale. It does
+    NOT reliably resolve on the host itself or inside the container,
+    and when it fails the client returns
+    ``{"status": "unavailable", "fail_open": true}`` — the right
+    diagnosis when that happens is to set ATOCORE_BASE_URL explicitly
+    to 127.0.0.1:8100 and retry.
+
+ATOCORE_TIMEOUT_SECONDS
+    Request timeout for most operations (default: 30).
+
+ATOCORE_REFRESH_TIMEOUT_SECONDS
+    Longer timeout for project refresh operations which can be slow
+    (default: 1800).
+
+ATOCORE_FAIL_OPEN
+    When "true" (default), network errors return a small fail-open
+    envelope instead of raising. Set to "false" for admin operations
+    where you need the real error.
 """
 
 from __future__ import annotations