Qualify CLI transfers and retain applied client-tools evidence

adoption/bootstrap.md

@@ -406,9 +406,9 @@ GitHub-hosted macOS runner; see
    UV_TOOL_DIR="$eco/python-tools" UV_TOOL_BIN_DIR="$eco/bin" \
      uv tool install --python 3.13 git+https://github.com/oraios/serena@c6fbd1c5932df2494ffa0020af5a9fbe80b82143
    UV_TOOL_DIR="$eco/python-tools" UV_TOOL_BIN_DIR="$eco/bin" \
-     uv tool install --python 3.13 jcodemunch-mcp==1.108.319
+     uv tool install --python 3.13 'jcodemunch-mcp[watch]==1.108.330'
    "$eco/bin/serena" --version           # Serena 2.0.0.dev0
-   "$eco/bin/jcodemunch-mcp" --version   # jcodemunch-mcp 1.108.319
+   "$eco/bin/jcodemunch-mcp" --version   # jcodemunch-mcp 1.108.330
    ```
    Then run the installer:
    ```sh

adoption/hooks/claude/token-lanes-block.main.md

@@ -5,6 +5,6 @@ TOKEN LANES, MAIN SESSION (source: docs/token-session-handbook.md, "Token lanes
 - For output above about 5 KB (tests, logs, diffs, listings, JSON), use ctx_batch_execute with queries or ctx_execute with intent. Print only the derived answer; keep failures and the path back to the full output.
 - Keep short, fixed-size output in Bash. RTK rewrites supported Bash calls automatically; Read, Grep and Glob bypass RTK.
 - Delegate a step whose only product is a conclusion (a survey, a file digest, a multi-file search) to a subagent; it receives its role block automatically.
-- For code questions, if exposed: Serena find_symbol and find_referencing_symbols for exact symbols, jcodemunch route (no execute), socraticode or semble for conceptual search, codebase-memory trace_path for call paths. Open the original source before judging or editing.
+- For code questions, if exposed: Serena find_symbol and find_referencing_symbols for exact symbols, jcodemunch route (no execute), socraticode or semble for conceptual search, codebase-memory-mcp trace_path for call paths. Open the original source before judging or editing.
 - For prior decisions, use ai-memory memory_query (if exposed) as historical evidence only. A memory index line says what a file holds: read the one section you need, never the whole file.
 - Use one lane per artifact and never stack compressors. Claim savings only from the client's own counters.

adoption/hooks/claude/token-lanes-block.md

@@ -1,11 +1,11 @@
 TOKEN LANES (source: docs/token-session-handbook.md, "Token lanes carried into subagents").
-- Load deferred token tools in ONE ToolSearch call before first use: "select:mcp__plugin_context-mode_context-mode__ctx_execute,mcp__plugin_context-mode_context-mode__ctx_batch_execute,mcp__plugin_context-mode_context-mode__ctx_search,mcp__plugin_context-mode_context-mode__ctx_fetch_and_index,mcp__serena__find_symbol,mcp__serena__find_referencing_symbols"; append task-needed ids to that same call: mcp__jcodemunch__route,mcp__jcodemunch__menu,mcp__jcodemunch__order,mcp__socraticode__codebase_search,mcp__qmd__query,mcp__qmd__get,mcp__ai-memory__memory_query,mcp__codebase-memory__search_graph,mcp__codebase-memory__trace_path,mcp__headroom__headroom_compress,mcp__headroom__headroom_retrieve. ToolSearch returns only tools the agent is granted. Select names exposed by the active client.
+- Load deferred token tools in ONE ToolSearch call before first use: "select:mcp__plugin_context-mode_context-mode__ctx_execute,mcp__plugin_context-mode_context-mode__ctx_batch_execute,mcp__plugin_context-mode_context-mode__ctx_search,mcp__plugin_context-mode_context-mode__ctx_fetch_and_index,mcp__serena__find_symbol,mcp__serena__find_referencing_symbols"; append task-needed ids to that same call: mcp__jcodemunch__route,mcp__jcodemunch__menu,mcp__jcodemunch__order,mcp__socraticode__codebase_search,mcp__qmd__query,mcp__qmd__get,mcp__ai-memory__memory_query,mcp__codebase-memory-mcp__search_graph,mcp__codebase-memory-mcp__trace_path,mcp__headroom__headroom_compress,mcp__headroom__headroom_retrieve. ToolSearch returns only tools the agent is granted. Select names exposed by the active client.
 - Fetch pages with ctx_fetch_and_index; batch requests with concurrency for several URLs, then quote with ctx_search. Do not use WebFetch for evidence: it answers from a small fast model's reading of the page.
 - Use ctx_search with specific queries and limit <=3.
 - For output over ~5 KB, use ctx_batch_execute or ctx_execute with intent (indexes output; returns only titles/previews), then ctx_search; print derived answers, keep failures and original-output recovery. Pass ctx_execute cwd = your working directory for every language; without it, non-shell code runs at the server's project root (the coordinator's checkout) and its writes persist. Rust runs in temp; use absolute project paths. Open authorized scratch files from Python inside ctx_execute; ctx_execute_file enforces project boundaries (#852). Never bypass permissions.
 - Automatic RTK: a Bash call containing $(...), backticks, <(...), a redirect to a file or a heredoc is never rewritten. && chains and multi-line blocks are rewritten segment by segment. In a pipeline RTK rewrites a supported producer feeding cat, head or tail (git diff | head -n 5) or a final grep/rg stage, but not gh (gh pr view 1 | head -n 5 is not rewritten). Run heavy reads as their own call. Never directly prefix rtk before `git show REV:path`, `diff`, `git branch`, `git log`, `jq`, `cd`, or `find` on a possibly-missing path. Use native commands or `rtk proxy <cmd>` for exact bytes/exit status; process large results in ctx_execute.
 - Use Serena find_symbol / find_referencing_symbols for exact symbols and references; jcodemunch route(task, repo: ".") (no execute), menu(query?), order(action, own args) on indexed repos; socraticode codebase_search(query, projectPath) with explicit projectPath for conceptual questions. Open original source before judging or editing.
-- Use codebase-memory trace_path (include_evidence=true adds resolver class and confidence; this parameter is on trace_path, not search_graph) or search_graph for symbol/reference queries; treat edges below confidence 0.5 as unverified candidates, and verify exact caller lists with Serena find_referencing_symbols.
+- Use codebase-memory-mcp trace_path (include_evidence=true adds resolver class and confidence; this parameter is on trace_path, not search_graph) or search_graph for symbols/references; treat edges below confidence 0.5 as unverified candidates; verify callers with Serena find_referencing_symbols.
 - Use qmd query with collections (foundation-docs, foundation-adoption, us-equities-foundation, us-equities-catalog), then get a line window. Use ai-memory memory_query with workspace/project from .ai-memory.toml as historical evidence only, never authority.
 - Use TOON for uniform arrays of flat records (same keys in every item); keep compact JSON for nested or non-uniform data, where TOON can be larger (upstream README).
 - For large selected text, use headroom_compress, then headroom_retrieve for recovery; require fidelity and count the recovery cost.

adoption/mcp/claude-user.json

@@ -1,5 +1,5 @@
 {
-  "_comment": "User-scope MCP server templates for `claude mcp add --scope user`, drafted 2026-09-23 from the live host's ~/.claude.json mcpServers block (names, commands, args and env var NAMES only -- no credentials, tokens or host-specific secret values). ${HOME} and ${ECO_ROOT} are placeholders in this template's own convention (adoption/templates/*.template.*): render or substitute them for the target host before use; do not commit a rendered copy with literal paths back into this file. install_claude_profile.py renders only ${HOME} and ${ECO_ROOT} and registers each server here but installs none of them (adoption/bootstrap.md step 4a), and `claude mcp add` refuses a name that already exists. To change only some servers, remove each one that should change (`claude mcp remove <name> -s user`) and rerun `install_claude_profile.py --only mcp` without --replace-mcp: that flag re-registers every differing server, ai-memory included. Changed 2026-09-25: serena runs Serena's own `serena` console script. `uv tool install` links it into ${ECO_ROOT}/bin when Serena is installed at the stack pin with the bootstrap's uv-tool layout: UV_TOOL_DIR=\"${ECO_ROOT}/python-tools\" UV_TOOL_BIN_DIR=\"${ECO_ROOT}/bin\" uv tool install --python 3.13 git+https://github.com/oraios/serena@c6fbd1c5932df2494ffa0020af5a9fbe80b82143 (adoption/bootstrap.md step 4a runs it; no bootstrap pin installs Serena). The 2026-09-23 entry named ${ECO_ROOT}/bin/serena-context, a wrapper local to that host (it set SERENA_HOME) that nothing in this repository creates; Serena reads SERENA_HOME itself and defaults to ~/.serena. The ai-memory URL is this repository's default bind, 127.0.0.1:49374 (recipes/README.md `ai-memory serve --bind`, AI_MEMORY_URL in adoption/hosts/example.json); the host's user-scope registration must name the port its own ai-memory unit binds, so on another port run `claude mcp remove ai-memory -s user`, then `claude mcp add --scope user --transport http ai-memory http://127.0.0.1:<port>/mcp`. Changed 2026-09-25: the jcodemunch entry was removed, so that jCodeMunch was no longer registered at user scope, where its server instruction to prefer it over Read/Grep/Glob/Bash loaded into every session. Changed 2026-10-04: the entry is back, on the user's directive that every fresh session starts with the tools ready (docs/decisions/2026-10-04-new-wsl-jcodemunch-user-scope.md), with the documented opt-out of its anonymous savings counter in the env block; `jcodemunch-mcp init` is not run. A project opts in with `claude mcp add --scope local` or a .mcp.json entry (adoption/bootstrap.md step 4a; docs/decisions/2026-09-23-claude-user-profile.md, 2026-09-25 addendum), and the Codex user template keeps it project-scoped too. The installer only visits the servers named here, so a host that registered jcodemunch per project (`--scope local`) keeps that registration beside the user-scope one. Changed 2026-09-30: socraticode, headroom, codebase-memory and qmd join, so this file registers every server the SubagentStart carrier blocks (adoption/hooks/claude/token-lanes-block*.md: the general block and the five role blocks) name except context-mode, which its plugin supplies. Each runs the command, arguments and environment of its entry in adoption/templates/codex.config.template.toml (tests/test_install_claude_profile.py, McpCodexParityTests), with three differences: serena runs Serena's `claude-code` context; socraticode runs the npm bin link ${ECO_ROOT}/bin/socraticode that both bootstraps' install_npm create, because this installer renders no ${SOCRATICODE_VERSION} (1.15.0 on Linux, 1.14.0 on macOS), and node runs the link's target, the package's dist/index.js (--preserve-symlinks-main is off by default); and the Codex-only PATH and RTK_TELEMETRY_DISABLED are left out, as serena's entry always has. SocratiCode's QDRANT_URL and LMSTUDIO_URL name this repository's defaults, QDRANT_URL and EMBED_URL in adoption/hosts/example.json, like the ai-memory URL: the installer compares env NAMES only, so a host already registered with its own values is reported as matching and kept, and a host whose endpoints differ registers its own values by hand. Claude Code has no per-server start-up timeout; MCP_TIMEOUT sets one for every server (https://code.claude.com/docs/en/mcp), where Codex gives serena 60 s and socraticode 120 s. headroom carries the four offline variables of recipes/README.md's registration (headroom-ai 0.37.0 turns its usage beacon on by default). qmd serves the catalog index this repository names, native-agent-stack-catalog (AGENTS.md). codebase-memory was left out by decision on 2026-09-27 (docs/decisions/2026-09-27-claude-harness-settings.md, item 12, token gap codebase-memory-mcp#2); the 2026-09-30 addendum of docs/decisions/2026-09-26-stack-agents-role-dispatch.md supersedes that exclusion for this registration only. No platform pins file installs it yet, so a new host installs the pinned v0.11.0 release by hand (recipes/README.md) before the entry connects, and never runs its `install` subcommand, which edits client configs. The entry is the bare binary with no arguments, upstream's manual form (DeusData/codebase-memory-mcp v0.11.0 README, Manual MCP Configuration): each session's process is a frontend of one shared per-account daemon that the first session starts (the same README, Session Coordination Daemon), so it is never wrapped in a bounded runner, whose scope stop would also stop a daemon started inside it (a forked child keeps its parent's cgroup, cgroups(7)). No shipped agent's tool list gains its tools.",
+  "_comment": "User-scope MCP server templates for `claude mcp add --scope user`, drafted 2026-09-23 from the live host's ~/.claude.json mcpServers block (names, commands, args and env var NAMES only -- no credentials, tokens or host-specific secret values). ${HOME} and ${ECO_ROOT} are placeholders in this template's own convention (adoption/templates/*.template.*): render or substitute them for the target host before use; do not commit a rendered copy with literal paths back into this file. install_claude_profile.py renders only ${HOME} and ${ECO_ROOT} and registers each server here but installs none of them (adoption/bootstrap.md step 4a), and `claude mcp add` refuses a name that already exists. To change only some servers, remove each one that should change (`claude mcp remove <name> -s user`) and rerun `install_claude_profile.py --only mcp` without --replace-mcp: that flag re-registers every differing server, ai-memory included. Changed 2026-09-25: serena runs Serena's own `serena` console script. `uv tool install` links it into ${ECO_ROOT}/bin when Serena is installed at the stack pin with the bootstrap's uv-tool layout: UV_TOOL_DIR=\"${ECO_ROOT}/python-tools\" UV_TOOL_BIN_DIR=\"${ECO_ROOT}/bin\" uv tool install --python 3.13 git+https://github.com/oraios/serena@c6fbd1c5932df2494ffa0020af5a9fbe80b82143 (adoption/bootstrap.md step 4a runs it; no bootstrap pin installs Serena). The 2026-09-23 entry named ${ECO_ROOT}/bin/serena-context, a wrapper local to that host (it set SERENA_HOME) that nothing in this repository creates; Serena reads SERENA_HOME itself and defaults to ~/.serena. The ai-memory URL is this repository's default bind, 127.0.0.1:49374 (recipes/README.md `ai-memory serve --bind`, AI_MEMORY_URL in adoption/hosts/example.json); the host's user-scope registration must name the port its own ai-memory unit binds, so on another port run `claude mcp remove ai-memory -s user`, then `claude mcp add --scope user --transport http ai-memory http://127.0.0.1:<port>/mcp`. Changed 2026-09-25: the jcodemunch entry was removed, so that jCodeMunch was no longer registered at user scope, where its server instruction to prefer it over Read/Grep/Glob/Bash loaded into every session. Changed 2026-10-04: the entry is back, on the user's directive that every fresh session starts with the tools ready (docs/decisions/2026-10-04-new-wsl-jcodemunch-user-scope.md), with the documented opt-out of its anonymous savings counter in the env block; `jcodemunch-mcp init` is not run. A project opts in with `claude mcp add --scope local` or a .mcp.json entry (adoption/bootstrap.md step 4a; docs/decisions/2026-09-23-claude-user-profile.md, 2026-09-25 addendum), and the Codex user template keeps it project-scoped too. The installer only visits the servers named here, so a host that registered jcodemunch per project (`--scope local`) keeps that registration beside the user-scope one. Changed 2026-09-30: socraticode, headroom, codebase-memory and qmd join, so this file registers every server the SubagentStart carrier blocks (adoption/hooks/claude/token-lanes-block*.md: the general block and the five role blocks) name except context-mode, which its plugin supplies. Each runs the command, arguments and environment of its entry in adoption/templates/codex.config.template.toml (tests/test_install_claude_profile.py, McpCodexParityTests), with three differences: serena runs Serena's `claude-code` context; socraticode runs the npm bin link ${ECO_ROOT}/bin/socraticode that both bootstraps' install_npm create, because this installer renders no ${SOCRATICODE_VERSION} (1.15.0 on Linux, 1.14.0 on macOS), and node runs the link's target, the package's dist/index.js (--preserve-symlinks-main is off by default); and the Codex-only PATH and RTK_TELEMETRY_DISABLED are left out, as serena's entry always has. SocratiCode's QDRANT_URL and LMSTUDIO_URL name this repository's defaults, QDRANT_URL and EMBED_URL in adoption/hosts/example.json, like the ai-memory URL: the installer compares env NAMES only, so a host already registered with its own values is reported as matching and kept, and a host whose endpoints differ registers its own values by hand. Claude Code has no per-server start-up timeout; MCP_TIMEOUT sets one for every server (https://code.claude.com/docs/en/mcp), where Codex gives serena 60 s and socraticode 120 s. headroom carries the four offline variables of recipes/README.md's registration (headroom-ai 0.37.0 turns its usage beacon on by default). qmd serves the catalog index this repository names, native-agent-stack-catalog (AGENTS.md). codebase-memory was left out by decision on 2026-09-27 (docs/decisions/2026-09-27-claude-harness-settings.md, item 12, token gap codebase-memory-mcp#2); the 2026-09-30 addendum of docs/decisions/2026-09-26-stack-agents-role-dispatch.md supersedes that exclusion for this registration only. Changed 2026-10-06: codebase-memory-mcp is the canonical server key after the CC ran the pinned v0.11.0 binary's native install --skip-binary --clients=claude route and read back the vendor registration, context hooks, skill and three agents. This template records the registration shape only; it does not copy or recreate those vendor assets. The entry is the bare binary with no arguments, upstream's manual form (DeusData/codebase-memory-mcp v0.11.0 README, Manual MCP Configuration): each session's process is a frontend of one shared per-account daemon that the first session starts (the same README, Session Coordination Daemon), so it is never wrapped in a bounded runner, whose scope stop would also stop a daemon started inside it (a forked child keeps its parent's cgroup, cgroups(7)). The vendor's Scout/Verify/Audit agents use its native read-only graph tool sets; this template adds no unrelated project agent grant.",
   "mcpServers": {
     "ai-memory": {
       "type": "http",
@@ -63,7 +63,7 @@
         "DO_NOT_TRACK": "1"
       }
     },
-    "codebase-memory": {
+    "codebase-memory-mcp": {
       "type": "stdio",
       "command": "${ECO_ROOT}/bin/codebase-memory-mcp",
       "args": [],