feat(agents): support direct CLI workspaces

[Waishnav]

Subagent commands currently depend on MCP-injected workspace state, which prevents the same tooling from working naturally in Codex, Pi, OpenCode, Claude Code, and other local harnesses. This layer lets the daemon accept a workspace root without a workspaceId and resolves direct CLI scope from injected MCP context, then the Git root, then the current directory.

It also makes argument parsing strict: unknown options and the removed --thinking option fail clearly, while a literal option after -- remains part of the prompt. Session lists remain workspace-scoped in both MCP and direct CLI use.

This is layer 2 of 4, based on #212. The next layer is #214. Verified with the full test suite, TypeScript typecheck, and packaged build.

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[greptile-apps]

Greptile Summary

The PR enables local agent CLI commands to infer a workspace directly from the current Git repository without requiring an injected workspace ID. It also makes workspace IDs optional across the daemon protocol, manager, and store, tightens CLI option parsing, and increments the daemon protocol version.

• Adds direct CLI workspace-root inference and allowed-root validation.
• Supports root-scoped agent creation, lookup, continuation, and listing.
• Rejects ambiguous CLI options while preserving literal dash-prefixed prompts after --.
• Updates protocol, manager, store, and integration tests for optional workspace IDs.

Confidence Score: 4/5

The symlink-sensitive workspace validation should be fixed before merging because it prevents valid direct agent commands from operating inside configured allowed roots.

The new resolver validates Git and injected workspace paths lexically, so equivalent symlinked and canonical paths can be treated as different locations and valid commands fail before reaching the daemon.

Files Needing Attention: src/cli-workspace.ts

Important Files Changed

Filename	Overview
src/cli-workspace.ts	Adds direct workspace inference, but lexical allowed-root validation rejects valid symlink-equivalent repository paths.
src/cli.ts	Routes agent commands through inferred workspace context and introduces stricter, separator-aware JSON option parsing.
src/local-agent-manager.ts	Allows root-only agent scopes while retaining workspace-ID matching when an ID is supplied.
src/local-agent-daemon-protocol.ts	Updates protocol decoding so workspace IDs are optional in agent records and request scopes.
src/local-agent-store.ts	Supports nullable workspace IDs and existing root-only list filtering.
src/local-agent-targets.ts	Adds explicit option termination and rejects unrecognized dash-prefixed options.

Sequence Diagram

sequenceDiagram
    participant U as CLI user
    participant C as devspace agents
    participant W as Workspace resolver
    participant D as Agent daemon
    participant M as Agent manager/store
    U->>C: agents command
    C->>W: resolve env root or Git top-level
    W->>W: enforce configured allowed roots
    W-->>C: workspaceRoot + optional workspaceId
    C->>D: authenticated protocol v3 request
    D->>M: root/ID-scoped operation
    M-->>D: agent record(s) or scope error
    D-->>C: structured result

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