Document AgentSync gitignore modes and team workflows step by step

[yacosta738]

Summary

We are keeping [gitignore].enabled = true as the default, but the product needs much better documentation explaining exactly how both workflows work:

1. Default workflow: AgentSync manages .gitignore and collaborators recreate symlinks via agentsync apply / package-manager hooks
2. Opt-out workflow: teams disable gitignore management and commit symlinks intentionally

Right now the behavior exists, but the trade-offs and team instructions are not documented clearly enough.

Goal

Produce end-to-end docs that explain the full decision tree and repo lifecycle step by step.

Required documentation topics

• What .agents/ is and why it is the canonical source of truth
• What [gitignore].enabled = true does by default
• Why this is the current default
• What collaborators must do after cloning in the default workflow
• How to wire agentsync apply into prepare / install flows
• How to opt out by setting [gitignore].enabled = false
• How to intentionally commit symlinks instead
• Recommended git staging/commit flow after migration
• Common pitfalls and how to recover from them
• Cross-links from getting-started, configuration reference, and CLI docs

Acceptance criteria

• Documentation covers both workflows with explicit trade-offs
• Docs include concrete command examples and a recommended step-by-step migration flow
• Docs explain collaborator expectations for each mode
• Docs remain consistent with the current product default (enabled = true)
• At least getting-started, configuration reference, and CLI docs are updated or cross-linked appropriately

Notes

This subissue is intentionally documentation-heavy. The goal is to leave this area extremely clear for users and teammates.

[linear]

DALLAY-219