Fix init flags, paths, and add CLI alternatives - #1084

Fixes found during an end-to-end run of this README (azd 1.36.0, azure.ai.agents 1.0.0-beta.21, azure.ai.toolboxes 1.0.0-beta.11, az 2.91.0, northcentralus, 2026-10-20).

• Init flag and output folder: -m prints Flag --manifest has been deprecated, use --template/-t instead; switched to -t. Init creates the project in agent-framework-agent-with-foundry-toolbox-responses, so running from my-toolbox-agent gives ERROR: no project exists; to create a new project, run azd init. Added the cd, documented the default env name / -e, and noted there is no model prompt (model comes from azure.yaml).
• Language resource CLI alternative: added az cognitiveservices account create ... --kind TextAnalytics.
• Language role assignment CLI: added a snippet that assigns Cognitive Services Language Owner to the project managed identity.
• User identity / PAT requirement: with a service principal, tool listing fails with User identity authentication for this tool is not supported for this caller. User identity authentication requires a delegated Microsoft Entra user context with user object ID and tenant ID.; an invalid GITHUB_MCP_PAT fails with HTTP_400 ... Authorization header is badly formatted. Documented both, with a link to Troubleshooting.
• Working directory for Option 2 and scripts: uv sync from the project root fails with error: No pyproject.toml found in current directory or any parent directory; now says to run from src/agent-framework-agent-with-foundry-toolbox-responses (same for scripts/).

Docs-only; no code or azure.yaml changes.