fix(gateway): read_thoughts range/last queries now include branch thoughts

[glassBead-tc]

Summary

• Root cause: read_thoughts range, last N, and default queries used getThoughts() (main chain only). Branch thoughts were invisible despite get_structure and deep_analysis being fixed in PR fix(gateway): surface branch thoughts in get_structure, read_thoughts, deep_analysis #99.
• Fix: Changed all three query paths to use getAllThoughts() (main chain + branches), matching the fix already applied to get_structure and deep_analysis.

Test plan

• 4 new tests: range with branches, branch-only range, main-only range, last N with branches
• All 22 gateway tests pass (no regressions)
• All 13 branch-retrieval tests pass
• TypeScript compiles cleanly

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[greptile-apps]

Greptile Overview

Greptile Summary

This PR completes the branch visibility fix started in PR #99 by updating the remaining three query paths in read_thoughts to use getAllThoughts() instead of getThoughts().

Changes:

• Range queries now include branch thoughts (e.g., range [4, 8] returns main thoughts 4-5 + branch thoughts 6-8)
• Last N queries now include branch thoughts in the count
• Default queries (no parameters) now include branch thoughts in the last 5 results
• All three changes use the same getAllThoughts() method already implemented for get_structure and deep_analysis

Test coverage:

• 4 new tests verify range with branches, branch-only range, main-only range, and last N with branches
• All tests validate correct thought counts and thought numbers
• PR author confirms all 22 gateway tests and 13 branch-retrieval tests pass

Confidence Score: 5/5

• This PR is safe to merge with no issues found
• The changes are minimal, focused, and follow the exact same pattern established in PR fix(gateway): surface branch thoughts in get_structure, read_thoughts, deep_analysis #99. The implementation uses the existing getAllThoughts() method correctly across all three query paths. Comprehensive test coverage validates all scenarios. No breaking changes, security issues, or edge cases identified.
• No files require special attention

Important Files Changed

Filename	Overview
src/gateway/gateway-handler.ts	Changed three query paths in read_thoughts to use getAllThoughts() instead of getThoughts(), ensuring branch thoughts are included in range, last N, and default queries. Logic is correct and consistent with PR #99 fixes.
src/gateway/tests/branch-retrieval.test.ts	Added 4 comprehensive tests covering range with branches, branch-only range, main-only range, and last N with branches. Tests verify correct behavior across different query scenarios.

Sequence Diagram

sequenceDiagram
    participant Client
    participant Gateway as GatewayHandler
    participant Storage as ThoughtboxStorage
    participant Store as LinkedThoughtStore

    Note over Client,Store: Range Query Example: [4, 8]
    Client->>Gateway: read_thoughts(range: [4, 8])
    Gateway->>Storage: getAllThoughts(sessionId)
    Storage->>Store: getSessionNodes(sessionId)
    Note over Store: Returns ALL nodes<br/>(main chain + branches)
    Store-->>Storage: [nodes 1-10]
    Storage-->>Gateway: [thoughts 1-10]
    Gateway->>Gateway: Filter: t.thoughtNumber >= 4 && <= 8
    Note over Gateway: Returns: main 4-5 + branch 6-8
    Gateway-->>Client: {count: 5, thoughts: [4,5,6,7,8]}

    Note over Client,Store: Last N Query Example: last 3
    Client->>Gateway: read_thoughts(last: 3)
    Gateway->>Storage: getAllThoughts(sessionId)
    Storage->>Store: getSessionNodes(sessionId)
    Store-->>Storage: [nodes 1-10]
    Storage-->>Gateway: [thoughts 1-10]
    Gateway->>Gateway: Slice: allThoughts.slice(-3)
    Note over Gateway: Returns: thoughts 8, 9, 10
    Gateway-->>Client: {count: 3, thoughts: [8,9,10]}

    Note over Client,Store: Default Query (no params)
    Client->>Gateway: read_thoughts()
    Gateway->>Storage: getAllThoughts(sessionId)
    Storage->>Store: getSessionNodes(sessionId)
    Store-->>Storage: [nodes 1-10]
    Storage-->>Gateway: [thoughts 1-10]
    Gateway->>Gateway: Slice: allThoughts.slice(-5)
    Note over Gateway: Returns: last 5 thoughts
    Gateway-->>Client: {count: 5, thoughts: [6,7,8,9,10]}

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