feat: generalize MCP agent targets and refresh app icon

AGENTS.md

@@ -233,10 +233,14 @@ General principles (KISS, DRY, YAGNI, SOLID) as applied in this codebase. Match
 - `packages/mimir-core/skills/mimir-audio-summary/SKILL.md` is the optional bundled audio-summary skill.
 - `packages/mimir-core/skills/mimir-markdown-report/SKILL.md` is the optional bundled Markdown-report
   skill.
-- `mimir setup` must keep generating agent-specific MCP helpers for easy local use:
+- `mimir setup` must keep generating agent-specific MCP helpers for easy local use by default:
   `.mimir/claude-mcp-server.json` for `claude mcp add-json`, `.mimir/codex-mcp.toml` for Codex
   config layers, `.mimir/kimi-mcp.json` for Kimi, `.mimir/opencode.jsonc` for OpenCode, and
-  `.mimir/cline-mcp.json` for Cline.
+  `.mimir/cline-mcp.json` for Cline. Keep `--agents` available on setup/install-skill so a target
+  repository can generate only the helpers it uses and remove stale unselected helpers.
+- Keep `--mcp-name`, `--mcp-command`, and repeatable `--mcp-arg` available on setup/install-skill
+  so repositories can generate MCP helper files for a stable server name or local wrapper script
+  without post-processing `.mimir/`.
 - `mimir install-agent` owns native skill discovery for the main supported coding agents. Keep
   `--agents claude|codex|kimi|opencode|cline` targeted so a user can install only the agent they use,
   with project scope by default and user scope available through `--scope user`.

README.md

@@ -269,6 +269,12 @@ Fresh setup keeps local state under one ignored `.mimir/` folder:
 
 It detects the repository package manager and writes the MCP helper files with the right command:
 `pnpm exec mimir serve-mcp`, `npx mimir serve-mcp`, `yarn exec mimir serve-mcp`, or `bunx mimir serve-mcp`.
+When a repository needs a wrapper script or only a subset of agent helpers, make that explicit during
+setup:
+
+```bash
+pnpm exec mimir setup --agents claude,codex --mcp-name project-docs --mcp-command ./scripts/serve-mcp.sh
+```
 
 For the usual agent-first workflow, expose Mimir to the coding assistants used in the repository:
 
@@ -467,6 +473,7 @@ Use `mimir setup` for the normal path, or install only the agent layer later:
 
 ```bash
 pnpm exec mimir install-skill
+pnpm exec mimir install-skill --agents claude,codex --mcp-command ./scripts/serve-mcp.sh
 pnpm exec mimir install-agent --agents claude,codex,kimi,opencode,cline
 ```
 

docs/agent-integration.md

@@ -8,6 +8,21 @@ If `mimir setup` was not used, install the agent kit into a repository:
 pnpm exec mimir install-skill
 ```
 
+By default this writes helper files for every supported agent. To keep a repository focused on only
+the agents it uses, pass a comma-separated target list:
+
+```bash
+pnpm exec mimir setup --agents claude,codex
+pnpm exec mimir install-skill --agents claude,codex
+```
+
+If an agent must launch Mimir through a repository wrapper, generate the MCP helpers with that
+command:
+
+```bash
+pnpm exec mimir setup --agents claude,codex --mcp-name project-docs --mcp-command ./scripts/serve-mcp.sh
+```
+
 This creates:
 
 ```plain text
@@ -25,6 +40,10 @@ This creates:
 .mimir/README.md
 ```
 
+When `--agents` is used, Mimir keeps `.mimir/mcp.json`, the skill folders, and the shared guides, but
+only writes the selected agent helper files. Previously generated unselected helper files are
+removed from `.mimir/`.
+
 Agents that support skill folders can load `.mimir/skills/mimir/` for deep local RAG usage. Load
 `.mimir/skills/mimir-audio-summary/` only when an optional spoken summary is needed. Load
 `.mimir/skills/mimir-markdown-report/` when the user asks for a cited Markdown report, dossier,
@@ -85,7 +104,7 @@ usage summaries and uses the returned citations.
 From the target repository root:
 
 ```bash
-pnpm exec mimir setup
+pnpm exec mimir setup --agents claude
 pnpm exec mimir install-agent --agents claude
 claude mcp add-json --scope local mimir "$(cat .mimir/claude-mcp-server.json)"
 ```
@@ -100,7 +119,7 @@ config.
 From the target repository root:
 
 ```bash
-pnpm exec mimir setup
+pnpm exec mimir setup --agents codex
 pnpm exec mimir install-agent --agents codex
 cat .mimir/codex-mcp.toml
 ```
@@ -114,7 +133,7 @@ skills.
 From the target repository root:
 
 ```bash
-pnpm exec mimir setup
+pnpm exec mimir setup --agents kimi
 pnpm exec mimir install-agent --agents kimi
 kimi --mcp-config-file .mimir/kimi-mcp.json
 ```
@@ -129,7 +148,7 @@ Kimi's global MCP file if you intentionally want a global setup. If you prefer n
 From the target repository root:
 
 ```bash
-pnpm exec mimir setup
+pnpm exec mimir setup --agents opencode
 pnpm exec mimir install-agent --agents opencode
 cat .mimir/opencode.jsonc
 ```
@@ -141,7 +160,7 @@ Copy or merge the generated snippet into the OpenCode config layer you use for t
 From the target repository root:
 
 ```bash
-pnpm exec mimir setup
+pnpm exec mimir setup --agents cline
 pnpm exec mimir install-agent --agents cline
 cat .mimir/cline-mcp.json
 ```

docs/api-reference.md

@@ -57,6 +57,18 @@ import { setupProject } from "@jcode.labs/mimir"
 const result = await setupProject({ cwd: "/path/to/workspace", ingest: true })
 ```
 
+Use `agents`, `mcpServerName`, `mcpCommand`, and `mcpArgs` when setup should generate only selected
+agent helpers or launch MCP through a repository wrapper:
+
+```ts
+await setupProject({
+  cwd: "/path/to/workspace",
+  agents: ["claude", "codex"],
+  mcpServerName: "project-docs",
+  mcpCommand: "./scripts/serve-mcp.sh",
+})
+```
+
 Useful result fields:
 
 | Field | Meaning |
@@ -294,6 +306,9 @@ import { installSkill } from "@jcode.labs/mimir"
 const result = await installSkill({ cwd: "/path/to/workspace" })
 ```
 
+Pass the same `agents`, `mcpServerName`, `mcpCommand`, and `mcpArgs` options to refresh a targeted
+agent kit without re-running full setup.
+
 The installed skills are:
 
 - `mimir`

docs/cli-reference.md

@@ -32,6 +32,7 @@ Mimir ships two CLIs:
 | Command | Use it when |
 | --- | --- |
 | `mimir install-skill` | Copy portable agent skills and an MCP config snippet into `.mimir/`. |
+| `mimir install-agent --agents <list>` | Expose Mimir skills in native Claude, Codex, Kimi, OpenCode, or Cline discovery folders. |
 | `mimir skill-path` | Print the package-bundled skill path for agents that load installed package skills. |
 | `mimir serve-mcp` | Start the MCP stdio server for compatible agents. |
 
@@ -58,6 +59,10 @@ Mimir ships two CLIs:
 | Option | Applies to | Meaning |
 | --- | --- | --- |
 | `--project-root <path>` | all project-scoped `mimir` commands | Run against a specific local workspace instead of the current directory. |
+| `--agents <list>` | `setup`, `install-skill`, `install-agent` | Select agent helpers or native skill folders: `all`, `claude`, `codex`, `kimi`, `opencode`, `cline`, or a comma-separated list. |
+| `--mcp-name <name>` | `setup`, `install-skill` | Set the MCP server name used in generated helper files. |
+| `--mcp-command <command>` | `setup`, `install-skill` | Use a repository wrapper or custom executable as the generated MCP stdio command. |
+| `--mcp-arg <arg>` | `setup`, `install-skill` | Add one argument to `--mcp-command`; repeat for multiple arguments. Use `--mcp-arg=--flag` for dash-prefixed values. |
 | `--top-k <number>` | `search`, `ask`, `research`, `evaluate` | Number of passages to return or keep. |
 | `--fail-under <recall>` | `evaluate` | Exit non-zero only when recall is below a threshold from `0` to `1`; without this option evaluation remains strict and fails on any miss. |
 | `--days <number>` | `usage-report` | Number of recent days to include in the metadata-only usage summary. |

packages/mimir-core/README.md

@@ -60,6 +60,9 @@ cat .mimir/opencode.jsonc
 cat .mimir/cline-mcp.json
 ```
 
+Use `pnpm exec mimir setup --agents claude,codex --mcp-command ./scripts/serve-mcp.sh` when a
+repository should generate only selected MCP helpers or launch through a local wrapper.
+
 By default, Mimir keeps local config, raw documents, generated indexes, access logs, models, reports,
 audio, and agent helper files under a single ignored `.mimir/` project folder. It reports
 unsupported/skipped files during ingestion and reports supported files that produced no extractable