refactor(toolset): remove orphaned code-search toolset methods

[barredterra]

Summary

• Drop the five ask_alyfToolset wrapper methods search_code, read_code_file, ls, find, and grep. After the move to the Deep Agents source-code-analyzer subagent, code search runs against the /source/ virtual mount and these wrappers were no longer registered as agent tools and had no callers.
• The underlying tools.* functions remain, still used by tests and the VFS backend.

Context

Follow-up cleanup that was intended to ride on the previous deepagent-fixes PR but landed on the backport branches after that PR had already merged. This PR brings develop to parity with the version-15 / version-16 backport branches.

Test plan

• Edited file parses; no linter errors.
• Module imports cleanly; the five methods are gone.
• Full code-tools test module passes (34 tests), including the assertions that these tool names are absent from the parent tool list.

[greptile-apps]

Confidence Score: 5/5

Safe to merge — removes only dead wrapper methods with no remaining call-sites in the codebase.

The deletion is a pure subtraction of five methods that had already lost their registration as agent tools. No callers remain on ask_alyfToolset instances, the underlying tools.* functions are untouched, and the existing test suite explicitly asserts that these tool names are absent from the parent tool list, so the tests directly validate the intended post-state.

No files require special attention.

Sequence Diagram

%%{init: {'theme': 'neutral'}}%%
sequenceDiagram
    participant Agent as LLM Agent
    participant Runner as ask_alyfAgentRunner
    participant Subagent as source-code-analyzer subagent
    participant Tools as tools.* (VFS backend)

    Note over Agent,Tools: Before this PR (now removed)
    Agent->>Runner: call search_code / ls / find / grep / read_code_file
    Runner->>Tools: tools.search_code() etc.
    Tools-->>Runner: result
    Runner-->>Agent: result

    Note over Agent,Tools: After this PR (current state)
    Agent->>Runner: _build_subagents()
    Runner->>Subagent: register source-code-analyzer
    Agent->>Subagent: code search request (via /source/ VFS)
    Subagent->>Tools: tools.search_code() etc.
    Tools-->>Subagent: result
    Subagent-->>Agent: result

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sequenceDiagram
    participant Agent as LLM Agent
    participant Runner as ask_alyfAgentRunner
    participant Subagent as source-code-analyzer subagent
    participant Tools as tools.* (VFS backend)

    Note over Agent,Tools: Before this PR (now removed)
    Agent->>Runner: call search_code / ls / find / grep / read_code_file
    Runner->>Tools: tools.search_code() etc.
    Tools-->>Runner: result
    Runner-->>Agent: result

    Note over Agent,Tools: After this PR (current state)
    Agent->>Runner: _build_subagents()
    Runner->>Subagent: register source-code-analyzer
    Agent->>Subagent: code search request (via /source/ VFS)
    Subagent->>Tools: tools.search_code() etc.
    Tools-->>Subagent: result
    Subagent-->>Agent: result

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