Remove context.md and scope prompt.txt to checkpoint-only prompts

[gtrrz-victor]

Closes #571

Summary

• Remove context.md entirely — it was dead code (written during checkpointing but never consumed by any reader). Removes generation, writing, reading, and all test/doc references across 19 files.
• Scope prompt.txt to checkpoint-only prompts — previously stored all session prompts joined by ---, but every consumer only used the first or last. Now stores only prompts from the current checkpoint portion of the transcript.
• Net deletion of 542 lines of unnecessary code and complexity.

What changed

context.md removal:

• generateContextFromPrompts() function and all callers
• Context fields from WriteCommittedOptions, UpdateCommittedOptions, SessionContent, SessionFilePaths
• context.md blob creation/reading in committed.go
• createContextFile() from lifecycle.go
• GetSessionContext() and getCheckpointsForSession() (dead code)
• context.md fallback in getSessionDescriptionFromTree()
• ContextFileName constant from paths.go

prompt.txt scoping:

• Added extractCheckpointPrompts() that scopes transcript by agent type (JSONL/Gemini/OpenCode) before extracting prompts
• Updated extractSessionData() and extractSessionDataFromLiveTranscript() to use it
• Filesystem path in lifecycle.go was already checkpoint-scoped — no change needed

Backward compatibility:

• Old context.md files on entire/checkpoints/v1 are simply ignored (no reader)
• Old prompt.txt with all-session prompts still works with ExtractFirstPrompt()/extractLastPrompt()

Test plan

• go build ./... compiles cleanly
• mise run fmt — no formatting changes
• mise run test:ci — all unit + integration tests pass
• Manual: entire explain on a repo with existing checkpoints (backward compat)
• Manual: Create new session, commit, verify no context.md on committed branch
• Manual: entire rewind to verify session labels display correctly

🤖 Generated with Claude Code

[cursor]

PR Summary

Medium Risk
Changes the persisted checkpoint metadata shape and prompt extraction logic across multiple agents, which could affect checkpoint/rewind behavior and any consumers expecting full-session prompts. Backward compatibility relies on ignoring old context.md and tests covering the new prompt scoping.

Overview
Removes context.md from checkpoint metadata end-to-end (constants, on-disk generation, git blob write/read paths, and related fields in WriteCommittedOptions/UpdateCommittedOptions, SessionContent, and SessionFilePaths), along with associated redaction and tests.

Changes prompt.txt semantics to be checkpoint-scoped rather than full-session: condensation now slices the transcript from CheckpointTranscriptStart (agent-aware for JSONL vs Gemini/OpenCode) via new extractCheckpointPrompts, and integration/unit tests + docs are updated to assert the new behavior.

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[Copilot]

Pull request overview

This PR removes the dead-code context.md generation/storage/reading across the entire codebase and scopes prompt.txt to contain only the prompts from the current checkpoint portion of a session transcript (rather than all session prompts). It is a cleanup PR that nets -542 lines.

Changes:

• Remove context.md entirely: Deletes generateContextFromPrompts(), createContextFile(), GetSessionContext(), getCheckpointsForSession(), the Context fields from WriteCommittedOptions/UpdateCommittedOptions/SessionContent/SessionFilePaths, related git-blob creation/reading in committed.go, and the ContextFileName constant.
• Scope prompt.txt to checkpoint-only prompts: Introduces extractCheckpointPrompts() that slices the full transcript to the checkpoint portion (via transcript.SliceFromLine for JSONL agents or SliceFromMessage for Gemini/OpenCode) before extracting user prompts; updates extractSessionData() and extractSessionDataFromLiveTranscript() to use it.
• Update tests and docs: Removes tests for deleted functions, updates integration tests to assert checkpoint-scoped (not full-session) prompt content, and updates architecture docs and CLAUDE.md to reflect the new structure.

Reviewed changes

Copilot reviewed 19 out of 19 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
cmd/entire/cli/strategy/manual_commit_condensation.go	Adds extractCheckpointPrompts(); removes generateContextFromPrompts() and getCheckpointsForSession(); updates prompt extraction calls
cmd/entire/cli/strategy/manual_commit_hooks.go	Removes context generation and redaction in finalizeAllTurnCheckpoints
cmd/entire/cli/strategy/manual_commit_logs.go	Removes dead GetSessionContext() function and its imports
cmd/entire/cli/strategy/manual_commit_types.go	Removes Context field from ExtractedSessionData
cmd/entire/cli/strategy/common.go	Removes context.md fallback in getSessionDescriptionFromTree and the # markdown prefix stripping
cmd/entire/cli/checkpoint/checkpoint.go	Removes Context fields from WriteCommittedOptions, UpdateCommittedOptions, SessionContent, SessionFilePaths
cmd/entire/cli/checkpoint/committed.go	Removes context blob creation/reading in writeSessionToSubdirectory, UpdateCommitted, ReadSessionContent
cmd/entire/cli/paths/paths.go	Removes ContextFileName constant
cmd/entire/cli/lifecycle.go	Removes createContextFile() function and its call
cmd/entire/cli/checkpoint/checkpoint_test.go	Removes Context-related test assertions
cmd/entire/cli/checkpoint/committed_update_test.go	Removes Context-related test assertions
cmd/entire/cli/strategy/manual_commit_condensation_test.go	Removes generateContextFromPrompts tests; updates Gemini multi-checkpoint test
cmd/entire/cli/strategy/manual_commit_test.go	Updates assertions to verify checkpoint-scoped prompts instead of full-session prompts
cmd/entire/cli/integration_test/manual_commit_workflow_test.go	Updates integration tests to assert checkpoint-scoped prompt content
cmd/entire/cli/lifecycle_test.go	Removes createContextFile tests
cmd/entire/cli/benchutil/parse_tree_bench_test.go	Updates comment and capacity for 4-file structure
CLAUDE.md	Updates architecture doc to remove context.md references
docs/architecture/sessions-and-checkpoints.md	Updates checkpoint structure diagrams
docs/architecture/claude-hooks-integration.md	Updates hook behavior description

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