fix(init): prevent clobbering instruction files (GEMINI.md, RTK.md)

[bnaylor]

Problem

The current implementation of rtk init and rtk uninstall performs full file overwrites/deletions of instruction files like GEMINI.md and RTK.md. This leads to data loss if users have custom notes or configuration in those files.

Solution

• Introduced upsert_write_rtk_block to manage RTK's instruction block using <!-- rtk-instructions v2 --> markers.
• Introduced remove_rtk_block_from_file to only remove RTK's block during uninstalls, preserving other content.
• Updated run_gemini, run_default_mode, and run_codex_mode to use these safer functions.
• Ensured all file updates are atomic to prevent corruption.
• Added comprehensive unit and end-to-end tests for file-level block management.

Verification

• Added test_upsert_write_rtk_block and test_remove_rtk_block_from_file tests pass.
• Manually verified with rtk cargo test that existing tests are not regressed.

Fixes #834 (Referenced but not closed, as per user instructions).
Credit for the fix: Gemini CLI (with assistance from bnaylor).

[CLAassistant]

All committers have signed the CLA.

[pszymkowiak]

Hi! Two things needed before we can review:

1. Retarget to develop — this PR targets master, but all PRs should target develop. You can change the base branch in the PR settings (right sidebar).
2. Sign the CLA — if not already done, please sign at https://cla-assistant.io/rtk-ai/rtk

Thanks!

[bnaylor]

Thanks! Switched branches. CLA should be good.

[aeppling]

Hey

We are cleaning up the codebase and improving the project structure for better onboarding. As part of this effort, PR #826 reorganizes src/ from a flat layout into subfolders.

No logic changes — only file moves and import path updates.

What you need to do

Rebase your branch on develop when receiving this comment:

git fetch origin && git rebase origin/develop

Git detects renames automatically. If you get import conflicts, update the paths:

use crate::git;        // now: use crate::cmds::git::git;
use crate::tracking;   // now: use crate::core::tracking;
use crate::config;     // now: use crate::core::config;
use crate::init;       // now: use crate::hooks::init;
use crate::gain;       // now: use crate::analytics::gain;

Need help rebasing? Tag @aeppling