Move index database into .dexter/ folder

[JesseHerrick]

Continuation of #10. I couldn't push to @egze's PR since he made it on a fork, but I needed to add the .gitignore change and README updates.

Summary from #10:

• Moves the SQLite index from /.dexter.db to /.dexter/dexter.db so the repo root stays clean and future dexter artifacts have a dedicated scratch space.
• Existing databases migrate automatically on the next dexter init or LSP startup: legacy .dexter.db and its -shm/-wal siblings are deleted and a fresh index is built in the new folder. No user action required beyond updating their own .gitignore.
• All path knowledge is centralized in internal/store via new DBPath, DBDir, LegacyDBPath, and FindProjectRoot helpers. The duplicated root-marker walks in cmd/main.go and internal/lsp/server.go are gone; the LSP call sites now have an inline comment documenting why they intentionally don't pass mix.exs as an extra marker.
• Editor-extension repos (dexter-vscode, dexter-zed) continue to work via their existing mix.exs/.git fallback markers and can be updated separately.

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Note

Medium Risk
Moderate risk because it changes index location/root-detection used by both CLI and LSP and adds automatic deletion-based migration of legacy DB files, which could impact existing setups if path resolution is wrong.

Overview
Dexter now stores its index at .dexter/dexter.db instead of .dexter.db, creating the .dexter/ directory on open and writing a local .gitignore so projects no longer need to ignore DB artifacts manually.

Path/root resolution is centralized in internal/store via DBPath/DBDir/LegacyDBPath and FindProjectRoot; the CLI and LSP switch to these helpers (with the LSP intentionally not falling back to mix.exs to keep monorepo roots anchored on .dexter/ or .git).

On startup, store.Open now auto-migrates by deleting any legacy .dexter.db + WAL/SHM siblings and rebuilding in the new location; integration/unit tests and README/editor configs are updated accordingly.

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