Clarion Assistant v4.6.0

Custom MCP servers in the IDE pane (issue #26) + Codex config self-heal

v4.6 lets you expose your own MCP servers to the in-IDE Claude tabs without modifying the addin, and fixes a duplicate-key crash that could prevent the Codex backend from launching.

Custom MCP Servers in the IDE Pane

Plug your own MCP servers into the in-IDE Claude tabs alongside the three built-ins (clarion-assistant, project-hub, browser).

• Sidecar file — %APPDATA%\ClarionAssistant\mcp-extra.json is a standard mcpServers JSON object. Entries are merged into the generated mcp-config.json each time a Claude tab launches, so edits take effect on the next tab spawn without restarting the IDE.
• Settings → MCP Server page has a new "Custom MCP Servers in the IDE Pane" section with an Open button that creates the file from a commented template if missing, then shell-opens it. Always visible regardless of the External MCP Access toggle.
• Auto-approve — mcp__<server>__* is appended to --allowedTools for every sidecar entry, so user tools don't trigger permission prompts inside the IDE pane.
• Reserved-key protection — an mcp-extra.json entry that collides with a built-in key (clarion-assistant, project-hub, browser) is silently skipped; the addin's real entry always wins.
• Malformed-JSON resilience — a corrupted sidecar (trailing comma, stray brace, etc.) is logged and ignored. The tab still launches with the three built-ins.
• Empty-state safe — if the file doesn't exist, behavior is identical to v4.5: just the three built-ins, no errors.

Smoke-tested end-to-end with @modelcontextprotocol/server-everything against all four corners: happy path, collision, malformed JSON, missing file.

Codex config self-heal

Fixes a corruption mode where launching a Codex tab would error with duplicate key [mcp_servers.clarion-assistant] and refuse to start.

Codex CLI's TOML serializer silently drops trailing comments when it appends state tables (e.g. [tui.model_availability_nux]), which removed the addin's <<< end >>> marker comment. The next Clarion.Assistant launch then saw a begin marker with no matching end and appended a second managed block, producing duplicate [mcp_servers.clarion-assistant] tables.

• Self-healing rewrite — on every Codex launch CA now strips all CA markers (paired or orphan) and all [mcp_servers.clarion-assistant.*] sections anywhere in the file, lifts foreign tables out of any broken managed region, and appends one fresh canonical block. Even a config that's already broken (two begin markers, one end, duplicate tables) is cleaned up automatically on the next launch.
• No user action required — just relaunch a Codex tab and the file is repaired in place.

User Guide

The bundled User Guide is bumped to v1.2 and now documents the mcp-extra.json sidecar and the Codex CLI backend (added in v4.4, hardened in v4.6). Open from Help → User Guide or docs\ClarionAssistant-Guide.html.

Installer

ClarionAssistant-4.6.0-Setup.exe is EV-signed (Kennewick Computer Company / Sectigo) with an RFC 3161 timestamp countersignature, so SmartScreen reputation transfers immediately.

Closes #26.