v1.17.9 merge: v2 architecture follow-ups (packages/cli, server, core, v2 TUI) — not shipped in #964

## v1.17.9 merge — v2 architecture follow-ups (not shipped in PR #964)

PR #964 brings in OpenCode v1.17.9, which introduces a **v2 architecture** across new workspaces (`packages/cli`, `packages/server`, `packages/core`, the standalone v2 SDK, and v2-mode `packages/tui` hydration). **These packages are not wired into the shipped `@altimateai/altimate-code` binary**, which runs on the legacy Hono server + `packages/opencode`. The Codex reviewer raised the items below against that v2 code.

Tracking them here so the merge can land; they become actionable **if/when we adopt the v2 runtime**. Branding-related ones (Altimate CORS origins, `.altimate-code` config discovery, Altimate global paths) are tagged so they're not lost in that adoption.

Source: review threads on PR #964 (resolved there with a pointer to this issue).

### `packages/core` (22)

- **P1** `packages/core/src/plugin/agent.ts:114` — Restore bash safety rules for V2 agents
- **P1** `packages/core/src/tool/read.ts:57` — Require external-directory approval for absolute reads
- **P1** `packages/core/src/tool/read.ts:58` — Gate absolute reads with external-directory policy
- **P1** `packages/core/src/tool/write.ts:78` — Gate V2 mutations with sensitive_write
- **P2** `packages/core/src/config.ts:182` — Discover `.altimate-code` config directories
- **P2** `packages/core/src/config.ts:182` — Discover the branded project config directory
- **P2** `packages/core/src/config.ts:204` — Load inline config supplied by SDK helpers
- **P2** `packages/core/src/database/migration.ts:215` — Recheck migration ownership inside each transaction
- **P2** `packages/core/src/global.ts:0` — Use Altimate global storage paths
- **P2** `packages/core/src/global.ts:0` — Use the fork's global app directory
- **P2** `packages/core/src/instruction-context.ts:55` — Load configured instruction sources
- **P2** `packages/core/src/project/copy.ts:179` — Seed v2 project roots before creating copies
- **P2** `packages/core/src/project/copy.ts:196` — Constrain project-copy names to the destination
- **P2** `packages/core/src/session.ts:207` — Record project directories when creating sessions
- **P2** `packages/core/src/session.ts:268` — Apply subpath filters when listing project sessions
- **P2** `packages/core/src/session.ts:268` — Apply the subpath filter when listing sessions
- **P2** `packages/core/src/session/projector.ts:425` — Roll v2 step usage into session totals
- **P2** `packages/core/src/session/runner/llm.ts:183` — Wait for plugin boot before selecting the runner agent
- **P2** `packages/core/src/state.ts:63` — Publish update events after committing rebuilt state
- **P2** `packages/core/src/tool/application-tools.ts:53` — Release public tool registrations with the scope
- **P2** `packages/core/src/tool/bash.ts:142` — Enforce external-directory approvals for bash arguments
- **P2** `packages/core/src/tool/builtins.ts:27` — Register a V2 task tool for subagents

### `packages/server` (18)

- **P1** `packages/server/src/handlers.ts:51` — Wire SessionV2 to local execution
- **P1** `packages/server/src/handlers.ts:52` — Wire SessionV2 to the local executor
- **P2** `packages/server/src/cors.ts:3` — Allow Altimate hosted origins
- **P2** `packages/server/src/cors.ts:3` — Allow the branded web origin in CORS
- **P2** `packages/server/src/groups/event.ts:20` — Type SSE events as Event payloads
- **P2** `packages/server/src/groups/fs.ts:22` — Add a real path parameter for fs.read
- **P2** `packages/server/src/groups/fs.ts:22` — Expose the file path in the fs.read contract
- **P2** `packages/server/src/handlers/command.ts:8` — Wait for plugin boot before listing commands
- **P2** `packages/server/src/handlers/command.ts:8` — Wait for plugin boot before returning commands
- **P2** `packages/server/src/handlers/integration.ts:26` — Wait for plugin boot before listing integrations
- **P2** `packages/server/src/handlers/model.ts:22` — Only advertise models the runner can execute
- **P2** `packages/server/src/handlers/pty.ts:118` — Declare the PTY token header for SDK callers
- **P2** `packages/server/src/handlers/reference.ts:7` — Wait for plugin boot before listing references
- **P2** `packages/server/src/handlers/reference.ts:7` — Wait for reference plugins before listing references
- **P2** `packages/server/src/handlers/session.ts:73` — Honor client directory when creating sessions
- **P2** `packages/server/src/handlers/session.ts:73` — Honor request location when creating sessions
- **P2** `packages/server/src/handlers/skill.ts:7` — Wait for plugin boot before listing skills
- **P2** `packages/server/src/handlers/skill.ts:7` — Wait for skill plugins before listing skills

### `packages/cli` (14)

- **P1** `packages/cli/src/commands/handlers/serve.ts:19` — Return an authenticated client from SDK server helper
- **P1** `packages/cli/src/tui.ts:23` — Don't mask provider hydration as empty
- **P1** `packages/cli/src/tui.ts:23` — Populate legacy bootstrap data from V2 APIs
- **P1** `packages/cli/src/tui.ts:8` — Pass the active cwd into the TUI client
- **P2** `packages/cli/package.json:8` — Add the opencode bin alias
- **P2** `packages/cli/package.json:8` — Expose the command that SDK helpers spawn
- **P2** `packages/cli/src/commands/commands.ts:8` — Declare TUI launch arguments on the root command
- **P2** `packages/cli/src/commands/handlers/serve.ts:19` — Expose serve credentials to SDK clients
- **P2** `packages/cli/src/commands/handlers/serve.ts:20` — Keep serve output compatible with SDK startup
- **P2** `packages/cli/src/commands/handlers/serve.ts:21` — Emit the startup line the SDK waits for
- **P2** `packages/cli/src/tui.ts:10` — Forward parsed CLI args into the TUI
- **P2** `packages/cli/src/tui.ts:10` — Pass the current directory into the TUI
- **P2** `packages/cli/src/tui.ts:15` — Load built-in TUI plugins in the v2 launcher
- **P2** `packages/cli/src/tui.ts:7` — Load the user's TUI configuration

### `packages/tui` (21)

- **P1** `packages/tui/src/component/prompt/index.tsx:1089` — Send prompts through the V2 session route
- **P1** `packages/tui/src/component/prompt/index.tsx:1089` — Submit prompts through the v2 prompt endpoint
- **P1** `packages/tui/src/component/prompt/index.tsx:994` — Create new sessions through the v2 endpoint
- **P1** `packages/tui/src/context/project.tsx:42` — Bootstrap the TUI from implemented location routes
- **P1** `packages/tui/src/context/project.tsx:42` — Hydrate project state through implemented v2 APIs
- **P1** `packages/tui/src/context/sdk.tsx:139` — Subscribe to the v2 event stream
- **P1** `packages/tui/src/context/sync.tsx:709` — Hydrate open sessions through v2 APIs
- **P1** `packages/tui/src/context/sync.tsx:709` — Hydrate sessions through implemented V2 routes
- **P1** `packages/tui/src/routes/session/permission.tsx:432` — Reply to permissions through the v2 session endpoint
- **P2** `packages/tui/src/component/dialog-move-session.tsx:81` — Use an implemented route for project directories
- **P2** `packages/tui/src/component/dialog-provider.tsx:397` — Connect providers through v2 integration routes
- **P2** `packages/tui/src/component/dialog-session-list.tsx:250` — Route session deletion through a v2 endpoint
- **P2** `packages/tui/src/component/prompt/index.tsx:412` — Interrupt sessions through an implemented V2 route
- **P2** `packages/tui/src/component/prompt/move.tsx:131` — Move sessions through an implemented endpoint
- **P2** `packages/tui/src/component/prompt/move.tsx:36` — Create project copies without legacy generate-name
- **P2** `packages/tui/src/component/prompt/move.tsx:39` — Route copy-name generation to an implemented endpoint
- **P2** `packages/tui/src/context/sdk.tsx:142` — Subscribe to the V2 event stream
- **P2** `packages/tui/src/routes/session/index.tsx:584` — Compact sessions through the V2 session API
- **P2** `packages/tui/src/routes/session/permission.tsx:429` — Reply to V2 permission requests via the session API
- **P2** `packages/tui/src/routes/session/question.tsx:51` — Route question replies through the V2 session API
- **P2** `packages/tui/src/routes/session/question.tsx:54` — Answer questions through the v2 session endpoint

### `packages/sdk` (1)

- **P2** `packages/sdk/js/src/v2/client.ts:37` — Only add location query fields where declared

### `package.json` (2)

- **P2** `package.json:21` — Add new workspaces to the CI path filter
- **P2** `package.json:21` — Add new workspaces to the TS CI filter

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_Filed during PR #964 final review. Shipped-path findings from the same review were fixed in `c44e0a967a` (plugin non-function export guard; fff-bun patch re-key) or dispositioned as by-design (ACP YOLO opt-in; legacy-tool agent threading)._