refactor: Task 0.5 amendments — README/ARCHITECTURE sweep + main.py install hint + drop dead AGNES_SERVER_URL

ARCHITECTURE.md

@@ -116,14 +116,14 @@ Command-line tool `da` for sync, query, and admin operations.
 | Command | Role |
 |---------|------|
 | `da sync` | Trigger data sync |
-| `da query` | Run SQL against analytics.duckdb |
-| `da admin group *` | Manage user groups |
-| `da admin grant *` | Manage resource grants |
-| `da admin register-table` | Register tables in table_registry |
-| `da admin break-glass <user>` | Emergency admin access recovery |
+| `agnes query` | Run SQL against analytics.duckdb |
+| `agnes admin group *` | Manage user groups |
+| `agnes admin grant *` | Manage resource grants |
+| `agnes admin register-table` | Register tables in table_registry |
+| `agnes admin break-glass <user>` | Emergency admin access recovery |
 | `da tokens *` | Manage personal access tokens |
 | `da metrics *` | Business metric definitions |
-| `da skills *` | List/show bundled skills |
+| `agnes skills *` | List/show bundled skills |
 
 ### 5. Authentication (`app/auth/`)
 

README.md

@@ -49,7 +49,7 @@ The orchestrator scans `/data/extracts/*/extract.duckdb`, attaches each into `an
 
 The first three modes are what `da sync` distributes to analysts. The fourth is server-side only — analysts query Jira data through the same `da sync`-distributed parquets.
 
-Admins manage per-source registrations through the `/admin/tables` UI (per-connector tabs for BigQuery / Keboola / Jira) or the `da admin register-table` CLI; per-row "Manage access" deep-links to `/admin/access` for granting tables to user groups via `resource_grants(group, ResourceType.TABLE, table_id)`.
+Admins manage per-source registrations through the `/admin/tables` UI (per-connector tabs for BigQuery / Keboola / Jira) or the `agnes admin register-table` CLI; per-row "Manage access" deep-links to `/admin/access` for granting tables to user groups via `resource_grants(group, ResourceType.TABLE, table_id)`.
 
 Analysts get a closed loop with Claude Code: `da analyst setup` writes `<workspace>/.claude/settings.json` with SessionStart (`da sync --quiet`) and SessionEnd (`da sync --upload-only --quiet`) hooks so every Claude Code session starts with fresh RBAC-filtered parquets and ends with the session log uploaded back.
 
@@ -113,7 +113,7 @@ To enroll a new table for auto-sync, register it (or update its `query_mode`) an
 For BigQuery, register a `query_mode='materialized'` table with a SQL body:
 
 ```bash
-da admin register-table orders_90d \
+agnes admin register-table orders_90d \
     --source-type bigquery \
     --query-mode materialized \
     --query @docs/queries/orders_90d.sql \
@@ -156,7 +156,7 @@ pytest tests/ -v
 │   ├── keboola/            # Keboola: extractor.py (DuckDB extension) + client.py (fallback)
 │   ├── bigquery/           # BigQuery: extractor.py (remote-only via DuckDB BQ extension)
 │   └── jira/               # Jira: webhook + incremental parquet → extract.duckdb
-├── cli/                    # CLI tool (`da sync`, `da query`, `da admin`)
+├── cli/                    # CLI tool (`da sync`, `agnes query`, `agnes admin`)
 ├── services/               # Standalone services (scheduler, telegram_bot, ws_gateway, etc.)
 ├── scripts/                # Utility + migration scripts
 ├── config/                 # Configuration templates (instance.yaml.example)

cli/main.py

@@ -1,6 +1,6 @@
 """agnes — CLI tool for AI Data Analyst.
 
-Primary interface for AI agents. Install: uv tool install data-analyst
+Primary interface for AI agents. Install: uv tool install agnes-the-ai-analyst
 """
 
 from importlib.metadata import PackageNotFoundError

tests/test_cli_sync.py

@@ -209,7 +209,6 @@ class TestStreamDownloadAtomicAndRetry:
     def test_atomic_write_via_tmp_then_rename(self, tmp_path, monkeypatch):
         """Target file must not exist before os.replace runs; writes go to .tmp first."""
         monkeypatch.setenv("AGNES_CONFIG_DIR", str(tmp_path))
-        monkeypatch.setenv("AGNES_SERVER_URL", "http://localhost:9999")
 
         target = tmp_path / "x.parquet"
         observed_paths: list[str] = []
@@ -242,7 +241,6 @@ class TestStreamDownloadAtomicAndRetry:
     def test_retries_on_transient_error(self, tmp_path, monkeypatch):
         """Transient network errors (ConnectError) trigger retry; eventual success is transparent."""
         monkeypatch.setenv("AGNES_CONFIG_DIR", str(tmp_path))
-        monkeypatch.setenv("AGNES_SERVER_URL", "http://localhost:9999")
         monkeypatch.setenv("AGNES_STREAM_RETRIES", "3")
 
         target = tmp_path / "x.parquet"
@@ -277,7 +275,6 @@ class TestStreamDownloadAtomicAndRetry:
     def test_no_retry_on_4xx(self, tmp_path, monkeypatch):
         """4xx (auth, 404) must surface immediately — retries are for transient issues only."""
         monkeypatch.setenv("AGNES_CONFIG_DIR", str(tmp_path))
-        monkeypatch.setenv("AGNES_SERVER_URL", "http://localhost:9999")
 
         import httpx
         calls = {"n": 0}