fix: unify MCP and settings pipelines in cache build#8
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wpfleger96 merged 2 commits intomainfrom Apr 30, 2026
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Two independent pipelines (build_merged_settings and install_mcps) wrote to the same agent config files without coordination, causing status to show false-positive diffs for amp, codex, and gemini. The cache now represents the complete expected file state by merging managed MCPs during build_merged_settings via a _merge_managed_mcps hook. Also fixes: MCP install output missing per-agent labels, amp settings.json formatting mismatch, tool install output appearing before profile header, Claude Code UI settings (skipAutoPermissionPrompt) lost on cache rebuild, and work profile model variant (opus vs opus[1m]).
Codex's mcp_settings_key ("mcp_servers") and mcp_tracking_key
("_ai_agent_rules_managed") weren't in preserved_fields, so
get_cache_diff still produced false-positive diffs after the MCP/cache
unification — the same class of bug fixed for Amp and Gemini.
Rather than manually adding MCP keys to each agent's preserved_fields
(which is fragile and caused the Codex omission), adds an
_effective_preserved_fields property that dynamically extends the
static list with MCP keys from the agent's MCPManager. Also guards
_merge_managed_mcps against non-dict MCP entries, and restores dim
ALREADY_INSTALLED output with per-agent labels.
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ai-agent-rules installandinstall_mcpswrote to the same agent config files through independent pipelines with no coordination. This causedstatusto show false-positive diffs for amp, codex, and gemini after every install — the cache had settings but not MCPs, so the live files (which had MCPs added byinstall_mcps) always looked out of sync.The fix makes the settings cache the single source of truth for what each agent config file should contain. A
_merge_managed_mcps()hook now runs at the end ofbuild_merged_settings()to reconcile managed MCPs into the cache — adding, updating, and removing stale entries — so the cache and the live file are always consistent. A Codex-specific subtlety (tracking section vs. inline markers) required reading managed-entry identity from[_ai_agent_rules_managed].namesrather than per-entry_managedByfields.MCP keys that need to be preserved across cache rebuilds (
mcp_settings_key,mcp_tracking_key) are now derived dynamically from each agent'sMCPManagervia_effective_preserved_fields, rather than manually added to each agent'spreserved_fields. This prevents the class of bugs where a new agent's MCP key is missed (which happened with Codex'smcp_serversand_ai_agent_rules_managedduring initial implementation).Several related UX issues resolved in the same pass:
statusdiffs for non-symlink JSON files (amp, gemini) now normalize formatting before comparing, eliminating false diffs from whitespace differencesinstall_mcpsreturnsALREADY_INSTALLEDand skips file writes when nothing changed_merge_managed_mcpsguards against non-dict MCP entries to avoidAttributeErroron malformed user configsinstalloutputskipAutoPermissionPromptadded to Claude's base settings alongsideskipDangerousModePermissionPromptwork.yamlprofile model corrected toopus[1m]to stop cache rebuilds overwriting the 1M context variant