Hot-reload all current ZeroSyntax settings

[ViTeXFTW]

Summary

• centralize and hot-reload all runtime ZeroSyntax settings
• dynamically register formatting and prevent stale debounced diagnostics
• replace workspace indexes when schema or base roots change
• synchronize VS Code configuration without restarting the server
• extend stdio and extension coverage and update settings documentation

Impact

Analysis and formatting settings now apply to open documents without restarting. Schema and base-root changes rebuild current workspace state with progress reporting. Only changing the server executable path restarts the language server.

Validation

• cargo test
• cargo build -p zerosyntax-server
• python crates/server/tests/e2e.py target/debug/zerosyntax-lsp.exe
• npm run compile --prefix editors/vscode
• npm run compile:test --prefix editors/vscode

The VS Code Electron test runner downloaded a Code.exe that rejects the harness flags before extension loading; source and test compilation pass. No large map corpus was available for typing_latency.py.

[greptile-apps]

Greptile Summary

This PR adds hot-reload support for ZeroSyntax runtime settings. The main changes are:

• Centralized runtime settings parsing in the LSP backend.
• Hot-reloaded analysis, formatting, debounce, schema, and base-root settings.
• Dynamic formatting registration for clients that support it.
• Workspace index replacement when schema or base roots change.
• VS Code configuration sync without restarting the server except for executable path changes.
• Expanded E2E and VS Code smoke coverage for the new runtime behavior.
• Updated language-server and VS Code documentation for the new settings flow.

Confidence Score: 5/5

This PR appears safe to merge.

The reviewed changes consistently parse startup and runtime settings, refresh or rebuild affected server state, and include coverage for the main hot-reload paths. No verified functional or security issues were found.

No files require special attention.

T-Rex Logs

What T-Rex did

• Built the zerosyntax-server package with cargo build -p zerosyntax-server.
• Ran the stdio e2e harness against target/debug/zerosyntax-lsp and verified it completed successfully with hot-reload coverage for diagnostics, debounce, base roots, schema reparsing, and formatting registration.
• Reviewed the end-to-end transcript and confirmed the build and tests finished with exit code 0 and ALL E2E CHECKS PASSED, including explicit hot-reload confirmations.
• Prepared and linked artifacts from both proofs for reviewer access.

_{Ran code and verified through T-Rex}

Important Files Changed

Filename	Overview
crates/server/src/backend.rs	Centralizes runtime settings parsing and applies hot-reloaded analysis, formatting, schema, and base-root changes with index replacement and diagnostic refresh.
editors/vscode/src/extension.ts	Switches VS Code configuration synchronization to the root zerosyntax section and restarts only when the server executable path changes.
crates/server/tests/e2e.py	Extends the stdio E2E harness to cover runtime setting changes, dynamic formatting registration, base-root replacement, schema reload, and stale diagnostics.
editors/vscode/src/test/suite/smoke.test.ts	Adds smoke coverage for the bare-percentage quick fix and hot-reloaded diagnostics in the VS Code extension.
editors/vscode/package.json	Updates extension setting descriptions for hot-reload behavior, background reindexing, and the server-path restart exception.
docs/language-server.md	Documents initialization and runtime configuration behavior, dynamic formatting, and reindexing semantics for standalone LSP clients.
editors/vscode/README.md	Updates VS Code user-facing settings documentation to reflect hot-reload behavior and the reduced restart scope.
AGENTS.md	Updates internal architecture notes to describe runtime setting hot-reload, dynamic formatting registration, and rebuild behavior.

_{Reviews (2): Last reviewed commit: "Normalize VS Code settings sync" | Re-trigger Greptile}

[ViTeXFTW]

@greptileai