Tool invocation logging middleware

[mattdholloway]

Adds a sensible logging integration on top of the (currently unused) observability.Exporters scaffolding:

• pkg/github/logging_middleware.go ToolLoggingMiddleware times every tools/call and logs at Debug on success / Error on failure (Go error or IsError result). It enriches a *slog.Logger with mcp.method and mcp.tool, then stores it on the context via observability.ContextWithLogger so tool handlers pick up the request-scoped logger automatically from deps.Logger(ctx).

• pkg/observability/logger_context.go ContextWithLogger / LoggerFromContext helpers.

• pkg/observability/log_level.go ParseLogLevel for 'debug|info|warn|error'.

• --log-level flag / GITHUB_LOG_LEVEL env var Fills an obvious gap: previously levels were hard-coded (stderr=Info, file=Debug). The default behaviour is preserved when the flag is empty.

• Fix fmt.Fprintf(os.Stderr, ...) feature-flag check reporting in BaseDeps.IsFeatureEnabled / RequestDeps.IsFeatureEnabled — these previously bypassed the structured logger entirely.

Tool handler code is intentionally untouched. The middleware gives every tool a duration/outcome log line uniformly; tools that want richer structured logs can opt in via deps.Logger(ctx).

Tests cover the middleware (success / error / IsError / non-tool pass-through / missing deps), the context helpers, level parsing, and the BaseDeps.Logger(ctx) context fallback.

Co-authored-by: Copilot 223556219+Copilot@users.noreply.github.com

Summary

Why

Fixes #

What changed

MCP impact

• No tool or API changes
• Tool schema or behavior changed
• New tool added

Prompts tested (tool changes only)

Security / limits

• No security or limits impact
• Auth / permissions considered
• Data exposure, filtering, or token/size limits considered

Tool renaming

• I am renaming tools as part of this PR (e.g. a part of a consolidation effort)
  • I have added the new tool aliases in deprecated_tool_aliases.go
• I am not renaming tools as part of this PR

Note: if you're renaming tools, you must add the tool aliases. For more information on how to do so, please refer to the official docs.

Lint & tests

• Linted locally with ./script/lint
• Tested locally with ./script/test

Docs

• Not needed
• Updated (README / docs / examples)