chore: remove internal docs from repo and sanitize references for handoff

Untrack thoughts/ (tasks, plans, grant text, reference docs) and
.claude/commands/linear.md from Git — files stay on disk, added to
.gitignore. Clean grant/Linear/ticket references from README, CLAUDE.md,
AGENTS.md, agent_docs, and src comments. Folder-level thoughts/ refs in
.claude commands kept for local workflow.

Author: jeffersonBastos

.claude/commands/describe_pr.md

@@ -18,7 +18,7 @@ You are tasked with generating a comprehensive pull request description followin
 ## Workflow Steps
 
 1. **Check for a PR description template:**
-   - Look for `thoughts/shared/pr_description.md` or similar template
+   - Look for a PR description template under `thoughts/shared/` (local) or similar
    - If no template exists, use the default format below
 
 2. **Identify the PR to describe:**