fix(mcp): honor AGENTMEMORY_TOOLS from .env in getVisibleTools

[ccf]

What

getVisibleTools() in src/mcp/tools-registry.ts read process.env["AGENTMEMORY_TOOLS"] directly, bypassing getMergedEnv() — the { ...fileEnv, ...process.env } helper that every other config reader reaches through getEnvVar(). This routes the lookup through getEnvVar() instead.

Why

AGENTMEMORY_TOOLS=all set in ~/.agentmemory/.env was silently ignored. The MCP tool surface stayed at the 8-tool core set instead of the full surface, even though .env.example documents that variable as the way to opt in:

AGENTMEMORY_TOOLS=all   # core (default) | all — surface exposed to MCP clients

Because getMergedEnv() is { ...fileEnv, ...process.env }, process.env (shell export, the --tools flag) still takes precedence over the file — only the missing .env fallback is restored.

This is the root cause behind #553: the "8 tools, not 51" state is the server returning its core surface over a working proxy — not a probe/proxy failure. It may also explain #400 (Codex full-surface) where a healthy server still serves the reduced set.

To be clear about scope: this does not address #510, which is the distinct "literal ${AGENTMEMORY_URL} placeholder breaks the shim's localhost fallback" connection bug — that one is already handled on main by the resolveEnvOrEmpty guard in #588.

How to verify

# with AGENTMEMORY_TOOLS=all only in ~/.agentmemory/.env (not exported):
# before — server reports 8 core tools; after — full surface

Automated coverage added in test/tools-visibility-env.test.ts (hermetic; sandboxes HOME and writes a temp .env):

• AGENTMEMORY_TOOLS=all in .env → full surface (getAllTools().length, incl. memory_graph_query)
• unset → core subset (regression guard)
• process.env overrides the .env value (precedence preserved)

npm run build is clean and the suite passes (the 5 unrelated auto-compress / embedding-provider failures only occur when a real ~/.agentmemory/.env is present in the test environment; they pass with a clean HOME).

Fixes #553

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