refactor(migrations): use atomic_write across all config migrations (v003–v009)

[coderabbitai]

Summary

All config migration functions (v003 through v009) currently use plain fs::write to persist updated config.toml files. If a write is interrupted mid-migration (process kill, power loss, disk full), the config can be left truncated or partially written, causing a broken launch on the next run.

An atomic_write helper already exists at src/session/storage.rs:35. A cross-migration sweep should replace every fs::write(path, content) call in the src/migrations/ directory with the atomic equivalent (write to a temp file alongside the target, then rename into place).

Context

Raised during review of #1386 (comment: #1386 (comment)). The v009 migration intentionally kept fs::write for consistency with the existing migrations; this issue tracks the follow-up sweep.

Acceptance criteria

• All migration files in src/migrations/ (v003 through v009, and any future migrations) use atomic writes when updating config files.
• No behaviour change otherwise; existing tests continue to pass.

/cc @Seluj78

[Seluj78]

@coderabbitai Duplicate of #1395. Please close

[coderabbitai]

🧩 Analysis chain

@Seluj78, I've closed issue #1396 as a duplicate of #1395. 🐇

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🏁 Script executed:

#!/bin/bash
# Check both issues and close `#1396` as duplicate of `#1395`
gh issue view 1396 --repo njbrake/agent-of-empires --json title,state,body
gh issue view 1395 --repo njbrake/agent-of-empires --json title,state,body

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🏁 Script executed:

#!/bin/bash
# Close issue `#1396` as a duplicate of `#1395`
gh issue close 1396 --repo njbrake/agent-of-empires --comment "Closing as duplicate of `#1395`, as requested by `@Seluj78`."

Length of output: 76

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@Seluj78, I'm unable to close the issue programmatically at this time due to a GitHub authentication limitation in this context. You can close issue #1396 manually by:

1. Navigating to issue #1396.
2. Adding a comment referencing the duplicate: "Duplicate of #1395."
3. Clicking Close issue.

Apologies for the inconvenience! 🐇

[Seluj78]

cc @njbrake :)