[bug] Generated Pi adapter uses deprecated positional raw JSON instead of stdin

[madebymlai]

Version

• Released binary: codebase-memory-mcp 0.10.8
• Also present on current main at 010569fa6ce1bc5d6430f858129243ea1a2e3fd5 (merged PR fix(pi): emit parameters and execute in the generated pi adapter #1678)

Platform

Linux (x64)

Install channel

GitHub release archive / install.sh

Binary variant

standard

What happened, and what did you expect?

The generated Pi extension (~/.pi/agent/extensions/cbmem.ts) invokes every tool by placing serialized JSON in a positional CLI argument:

spawn(BIN, ['cli', '--json', tool, JSON.stringify(args ?? {})], {
  stdio: ['ignore', 'pipe', 'pipe'],
  // ...
});

The CLI itself declares this argument form deprecated and writes a warning to stderr on every call:

warning: passing raw JSON to 'cli list_projects' is deprecated and will be removed in a future release; use flags (run 'cli list_projects --help'), --args-file <path>, or piped stdin.

The README also says inline JSON is retained only for backward compatibility and recommends flags, --args-file, or stdin.

I expected the generated adapter to use one of the supported non-deprecated transports. Since this is a programmatic bridge and already owns a child stdin pipe, stdin is the simplest option.

There are two related but distinct effects:

1. v0.10.8 functional failure: the released generator does not include CLI --json. It tries to JSON.parse the default human-readable tree output, fails, and then surfaces the stderr deprecation warning as the tool error. Passing tool argument format:"json" makes some tools appear to work only because their stdout becomes parseable JSON. Tools without that format option (query_graph, get_architecture, search_code) remain unusable through the wrapper.
2. Current main after fix(pi): emit parameters and execute in the generated pi adapter #1678: PR fix(pi): emit parameters and execute in the generated pi adapter #1678 correctly adds CLI --json, so the full MCP envelope is parseable and fixes the functional failure. However, the generated adapter still passes the request JSON positionally, so it still exercises the deprecated path and emits the warning on every invocation. It will break when the compatibility path is removed.

This issue is therefore narrower than #1806 / #1678: the tool schema/result-envelope work there is correct; this reports the remaining request transport.

Reproduction

No indexed or proprietary repository is required to reproduce the remaining main-branch problem.

Deprecated path used by the generated adapter:

CBM_LOG_LEVEL=error codebase-memory-mcp cli --json list_projects '{}'

Result: exit 0 and valid stdout, but stderr contains:

warning: passing raw JSON to 'cli list_projects' is deprecated and will be removed in a future release; use flags (run 'cli list_projects --help'), --args-file <path>, or piped stdin.

Documented stdin path:

printf '{}' | CBM_LOG_LEVEL=error codebase-memory-mcp cli --json list_projects

Result: exit 0, the same valid MCP envelope on stdout, and empty stderr.

I also verified stdin + --json with default tree output for search_graph, query_graph, and get_architecture. All return a valid MCP envelope; no tool-level format:"json" argument is needed.

Suggested fix

Generate the bridge with a writable stdin and remove the positional JSON argument:

const child = spawn(BIN, ['cli', '--json', tool], {
  stdio: ['pipe', 'pipe', 'pipe'],
  env: { ...process.env, CBM_LOG_LEVEL: 'error' },
});

child.stdin.on('error', () => {
  // The child may close stdin early after an abort or startup failure.
});
child.stdin.end(JSON.stringify(args ?? {}));

Sending {} and closing stdin also works for list_projects; as documented, that tool does not consume stdin and remains responsive.

Suggested regression assertions:

• generated Pi adapter contains ['cli', '--json', tool]
• generated Pi adapter uses stdio: ['pipe', 'pipe', 'pipe']
• generated Pi adapter ends stdin with serialized args
• generated Pi adapter does not append JSON.stringify(args ?? {}) to argv
• smoke the generated adapter with a default tree-format tool and a tool without a format parameter (query_graph is suitable)
• assert stderr does not contain the raw-JSON deprecation warning

Local workaround verified

I patched the generated extension to use --json plus stdin and to pass the MCP envelope's content through to Pi. A Jiti-loaded fixture registered all 15 tools and verified:

• default-tree search_graph renders results
• default-tree query_graph renders results
• structured envelope details are preserved
• MCP error envelopes throw a Pi tool error
• no explicit tool-level format:"json" is required

Note: reinstall/update may overwrite the local extension until the generator ships the change.

Confirmations

• I searched existing issues; [bug] Auto-generated Pi extension (cbmem.ts) missing parameters schema — crashes on startup #1806 / PR fix(pi): emit parameters and execute in the generated pi adapter #1678 address the adjacent Pi schema and result-envelope problem, not stdin transport.
• The reproduction requires no proprietary code or logs.

[madebymlai]

One important symptom clarification from the original Pi tool smoke test:

Through the v0.10.8 generated Pi adapter, affected tool calls appear to return only the deprecation warning, with no query result.

Observed matrix:

Pi tool call	Observed result
search_graph with default/tree output	warning only
search_graph with tool arg format:"json"	correct results
detect_changes with default/tree output	warning only
detect_changes with tool arg format:"json"	correct results
query_graph	warning only
get_architecture	warning only
search_code	warning only

The distinction is that the underlying CLI is not warning-only. Running the equivalent command directly produces:

• valid tree result on stdout;
• raw-JSON deprecation warning on stderr;
• exit code 0.

The generated adapter then:

1. tries to parse each stdout line with JSON.parse;
2. cannot parse the valid human-readable tree output;
3. finds no JSON response;
4. reports err.trim() as the failure message.

Because stderr contains the deprecation warning, that warning becomes the only text Pi/its agent sees. This makes the issue look like the upstream graph tool returned no data, even though its valid result was present on stdout and discarded by the adapter.

CLI --json fixes the result parsing by wrapping tree text in an MCP JSON envelope. Sending request arguments over stdin separately removes the warning.

[madebymlai]

Classification note: this is not a graph extraction/parsing-quality defect. It is a functional Pi editor/integration bug. The adapter discards valid stdout and makes query_graph, get_architecture, and search_code unusable; default calls to other tree-format tools also fail unless they happen to support the accidental format:"json" workaround. Suggested labels: bug + editor/integration rather than parsing/quality. I cannot change labels in this repository.