Add workflow update step to upgrade command

[Copilot]

The upgrade command was not updating workflows from their source repositories before compilation, causing workflows with source fields to remain outdated after an upgrade.

Changes

• Added Step 2 to upgrade flow: calls UpdateWorkflows() after updating agent files
• Updated documentation to reflect new 4-step process in help text
• Non-critical failure handling: upgrade continues if no workflows have source fields or updates fail

New Upgrade Flow

1. Update agent files
2. Update workflows (workflows with 'source' field)  ← NEW
3. Apply codemods
4. Compile workflows
5. Push changes (if --push)

Example Output

ℹ Updating agent and prompt files...
✓ Updated agent and prompt files
ℹ Updating workflows from source repositories...
🔍 Skipping workflow-a: no source field
ℹ Found 1 workflow(s) to update
ℹ Updating workflow: workflow-b
✓ Updated workflow-b from v1.0.0 to v1.1.0
ℹ Applying codemods to all workflows...
ℹ Compiling all workflows...
✓ Upgrade complete

Respects --no-fix flag: skips workflow updates along with codemods and compilation.

Original prompt

The "upgrade" command should also run "update" before running "compile".

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[pelikhan]

@copilot run update after codemods