Merge V3 seed and coverage fixes from system-prompt parent

Preserve valid native V3 system heads in resumed fixture seeds and inherit the scanner coverage repair. Regenerate only upper-layer owner-local expected output through the actual loop so fallback title follows header/context. All five affected expected cases pass refresh; no historical Session generation or assertion is weakened.

apps/cli/tests/profiles/headless/tests/expected/semantic-checkpoint/session.expected.jsonl

@@ -1,10 +1,11 @@
 {"type":"session","version":3,"id":"{{sessionId}}","createdAt":0,"cwd":"{{cwd}}","isSeeded":false,"delegationDepth":0}
 {"type":"turn/start","data":{"turn":1}}
-{"type":"user/message","data":{"content":[{"type":"text","text":"Perform one side-effecting remote mutation."}],"source":{"kind":"user"},"role":"user","id":"{{sessionId}}"},"surfaceOp":"append"}
 {"type":"step/start","data":{"turn":1,"step":1}}
+{"type":"system/message","data":{"turn":1,"step":1,"message":{"role":"system","content":[],"source":{"kind":"plugin","plugin":"@deepseek-ai/dsh-system-prompt"},"id":"{{sessionId}}"}},"surfaceOp":"append"}
+{"type":"user/message","data":{"content":[{"type":"text","text":"Perform one side-effecting remote mutation."}],"source":{"kind":"user"},"role":"user","id":"{{sessionId}}"},"surfaceOp":"append"}
 {"type":"assistant/message","data":{"turn":1,"step":1,"stream":[],"message":{"role":"assistant","content":[{"type":"tool-call","id":"unknown-outcome-call","name":"write_remote","arguments":"{\"value\":1}"}],"source":{"kind":"model","provider":"deepseek-official","model":"deepseek-v4-flash"},"id":"{{sessionId}}"}},"surfaceOp":"append"}
 {"type":"tool/call","data":{"turn":1,"step":1,"callId":"unknown-outcome-call","name":"write_remote","arguments":"{\"value\":1}"}}
-{"type":"tool/result","data":{"turn":1,"step":1,"message":{"id":"interrupted-tool-result-unknown-outcome-call-5","role":"user","source":{"kind":"tool","callId":"unknown-outcome-call"},"content":[{"type":"tool-result","toolCallId":"unknown-outcome-call","isError":true,"content":[{"type":"text","text":"The tool call was interrupted after it was recorded, but no result was durably recorded. Its outcome is unknown. Decide whether to retry from the tool semantics: retry only if the operation is read-only or idempotent; if it may have side effects, first verify external state or ask the user. Do not retry blindly."}]}]},"error":{"name":"ToolOutcomeUnknownError","code":"TOOL_OUTCOME_UNKNOWN"}},"surfaceOp":"append","sourceEventSeqs":[4]}
+{"type":"tool/result","data":{"turn":1,"step":1,"message":{"id":"interrupted-tool-result-unknown-outcome-call-6","role":"user","source":{"kind":"tool","callId":"unknown-outcome-call"},"content":[{"type":"tool-result","toolCallId":"unknown-outcome-call","isError":true,"content":[{"type":"text","text":"The tool call was interrupted after it was recorded, but no result was durably recorded. Its outcome is unknown. Decide whether to retry from the tool semantics: retry only if the operation is read-only or idempotent; if it may have side effects, first verify external state or ask the user. Do not retry blindly."}]}]},"error":{"name":"ToolOutcomeUnknownError","code":"TOOL_OUTCOME_UNKNOWN"}},"surfaceOp":"append","sourceEventSeqs":[5]}
 {"type":"step/end","data":{"turn":1,"step":1}}
 {"type":"turn/end","data":{"turn":1,"reason":{"kind":"interrupted"}}}
 {"type":"session/end-seed","data":{}}
@@ -15,12 +16,12 @@
 {"type":"turn/start","data":{"turn":2}}
 {"type":"agent/inbox/spliced","data":{"target":"next-turn","start":0,"removedCount":1,"inserted":[]}}
 {"type":"step/start","data":{"turn":2,"step":1}}
-{"type":"system/message","data":{"turn":2,"step":1,"message":{"role":"system","content":[{"type":"text","text":"{{system}}"}],"source":{"kind":"plugin","plugin":"@deepseek-ai/dsh-system-prompt"},"id":"{{sessionId}}"}},"surfaceOp":"append"}
+{"type":"system/message","data":{"turn":2,"step":1,"message":{"role":"system","content":[{"type":"text","text":"{{system}}"}],"source":{"kind":"plugin","plugin":"@deepseek-ai/dsh-system-prompt"},"id":"{{sessionId}}"}},"sourceEventSeqs":[2],"surfaceOp":{"op":"replace","start":2,"end":2}}
 {"type":"user/message","data":{"content":[{"type":"text","text":"Continue safely from the interrupted operation."}],"source":{"kind":"user"},"role":"user","id":"{{sessionId}}"},"surfaceOp":"append"}
 {"type":"user/message","data":{"content":[{"type":"text","text":"Current runtime context. This snapshot supersedes earlier runtime-context snapshots.\n\nCurrent DSH file policy: workspace-write. Any available operation enforced by the DSH file sandbox may modify files under the session workspace: \"{{cwd}}\". Some platform temporary areas may also be writable.\n\nApproval policy: ask. Operations that require approval may ask through the configured answerers; without an available answerer, the request fails closed."}],"source":{"kind":"plugin","plugin":"@deepseek-ai/dsh-system-prompt","form":"snapshot","sections":[{"name":"sandbox:policy","text":"Current DSH file policy: workspace-write. Any available operation enforced by the DSH file sandbox may modify files under the session workspace: \"{{cwd}}\". Some platform temporary areas may also be writable."},{"name":"approval:policy","text":"Approval policy: ask. Operations that require approval may ask through the configured answerers; without an available answerer, the request fails closed."}]},"role":"user","id":"{{sessionId}}"},"surfaceOp":"append"}
 {"type":"request/header","data":{"header":{"config":{"provider":"deepseek-official","model":"deepseek-v4-flash"},"tools":"{{tools}}"},"reason":"initial"}}
 {"type":"request/context","data":{"provider":"deepseek-official","model":"deepseek-v4-flash"}}
-{"type":"session/title","data":{"title":"Perform one side-effecting remote mutati","messageSeqs":[1],"source":{"kind":"fallback"}}}
+{"type":"session/title","data":{"title":"Perform one side-effecting remote mutati","messageSeqs":[3],"source":{"kind":"fallback"}}}
 {"type":"assistant/message","data":{"turn":2,"step":1,"message":{"role":"assistant","content":[{"type":"text","text":"I will verify the external state before deciding whether to retry the side-effecting operation."}],"source":{"kind":"model","provider":"deepseek-official","model":"deepseek-v4-flash"},"id":"{{sessionId}}"},"stream":[{"type":"chunk","time":0,"chunk":{"type":"block-start","index":0,"blockType":"text"}},{"type":"text-chunks","time0":0,"index":0,"dt":[],"texts":["I will verify the external state before deciding whether to retry the side-effecting operation."]},{"type":"chunk","time":0,"chunk":{"type":"block-end","index":0,"block":{"type":"text","text":"I will verify the external state before deciding whether to retry the side-effecting operation."}}},{"type":"chunk","time":0,"chunk":{"type":"finish","reason":{"kind":"stop"}}}]},"surfaceOp":"append"}
 {"type":"step/end","data":{"turn":2,"step":1}}
 {"type":"turn/end","data":{"turn":2,"reason":{"kind":"completed"}}}

apps/cli/tests/profiles/headless/tests/expected/subagent-diagnostic/parent.expected.jsonl

@@ -16,9 +16,9 @@
 {"type":"system/message","data":{"turn":2,"step":1,"message":{"role":"system","content":[{"type":"text","text":"{{system}}"}],"source":{"kind":"plugin","plugin":"@deepseek-ai/dsh-system-prompt"},"id":"{{sessionId}}"}},"sourceEventSeqs":[2],"surfaceOp":{"op":"replace","start":2,"end":2}}
 {"type":"user/message","data":{"content":[{"type":"text","text":"Call list_agents once and report what it shows."}],"source":{"kind":"user"},"role":"user","id":"{{sessionId}}"},"surfaceOp":"append"}
 {"type":"user/message","data":{"content":[{"type":"text","text":"Current runtime context. This snapshot supersedes earlier runtime-context snapshots.\n\nCurrent DSH file policy: workspace-write. Any available operation enforced by the DSH file sandbox may modify files under the session workspace: \"{{cwd}}\". Some platform temporary areas may also be writable.\n\nApproval policy: ask. Operations that require approval may ask through the configured answerers; without an available answerer, the request fails closed."}],"source":{"kind":"plugin","plugin":"@deepseek-ai/dsh-system-prompt","form":"snapshot","sections":[{"name":"sandbox:policy","text":"Current DSH file policy: workspace-write. Any available operation enforced by the DSH file sandbox may modify files under the session workspace: \"{{cwd}}\". Some platform temporary areas may also be writable."},{"name":"approval:policy","text":"Approval policy: ask. Operations that require approval may ask through the configured answerers; without an available answerer, the request fails closed."}]},"role":"user","id":"{{sessionId}}"},"surfaceOp":"append"}
-{"type":"session/title","data":{"title":"Start a background job.","messageSeqs":[3],"source":{"kind":"fallback"}}}
 {"type":"request/header","data":{"header":{"config":{"provider":"deepseek-official","model":"deepseek-v4-flash"},"tools":"{{tools}}"},"reason":"initial"}}
 {"type":"request/context","data":{"provider":"deepseek-official","model":"deepseek-v4-flash"}}
+{"type":"session/title","data":{"title":"Start a background job.","messageSeqs":[3],"source":{"kind":"fallback"}}}
 {"type":"assistant/message","data":{"turn":2,"step":1,"message":{"role":"assistant","content":[{"type":"tool-call","id":"list-once","name":"list_agents","arguments":"{}"}],"source":{"kind":"model","provider":"deepseek-official","model":"deepseek-v4-flash"},"id":"{{sessionId}}"},"usage":{"inputTokens":10,"outputTokens":5},"stream":[{"type":"chunk","time":0,"chunk":{"type":"block-start","index":0,"blockType":"tool-call"}},{"type":"tool-call-chunks","time0":0,"index":0,"dt":[],"id":"list-once","name":"list_agents","args":["{}"]},{"type":"chunk","time":0,"chunk":{"type":"block-end","index":0,"block":{"type":"tool-call","id":"list-once","name":"list_agents","arguments":"{}"}}},{"type":"chunk","time":0,"chunk":{"type":"usage","usage":{"inputTokens":10,"outputTokens":5}}},{"type":"chunk","time":0,"chunk":{"type":"finish","reason":{"kind":"tool-calls"}}}]},"surfaceOp":"append"}
 {"type":"tool/call","data":{"turn":2,"step":1,"callId":"list-once","name":"list_agents","arguments":"{}"}}
 {"type":"tool/result","data":{"turn":2,"step":1,"message":{"source":{"kind":"tool","callId":"list-once"},"content":[{"type":"tool-result","toolCallId":"list-once","content":[{"type":"text","text":"{{sessionId}} [diagnostic: corrupt]"}],"isError":false}],"role":"user","id":"{{sessionId}}"}},"sourceEventSeqs":[21],"surfaceOp":"append"}

apps/cli/tests/profiles/headless/tests/expected/subagent-inheritance/parent.expected.jsonl

@@ -17,9 +17,9 @@
 {"type":"system/message","data":{"turn":2,"step":1,"message":{"role":"system","content":[{"type":"text","text":"{{system}}"}],"source":{"kind":"plugin","plugin":"@deepseek-ai/dsh-system-prompt"},"id":"{{sessionId}}"}},"sourceEventSeqs":[2],"surfaceOp":{"op":"replace","start":2,"end":2}}
 {"type":"user/message","data":{"content":[{"type":"text","text":"Delegate the write probe to a subagent."}],"source":{"kind":"user"},"role":"user","id":"{{sessionId}}"},"surfaceOp":"append"}
 {"type":"user/message","data":{"content":[{"type":"text","text":"Current runtime context. This snapshot supersedes earlier runtime-context snapshots.\n\nCurrent DSH file policy: read-only. Any available operation enforced by the DSH file sandbox cannot modify files in the standing mode. Do not refuse a required modification from this policy alone: try an available tool normally and follow any denial and escalation guidance it returns.\n\nApproval policy: ask. Operations that require approval may ask through the configured answerers; without an available answerer, the request fails closed."}],"source":{"kind":"plugin","plugin":"@deepseek-ai/dsh-system-prompt","form":"snapshot","sections":[{"name":"sandbox:policy","text":"Current DSH file policy: read-only. Any available operation enforced by the DSH file sandbox cannot modify files in the standing mode. Do not refuse a required modification from this policy alone: try an available tool normally and follow any denial and escalation guidance it returns."},{"name":"approval:policy","text":"Approval policy: ask. Operations that require approval may ask through the configured answerers; without an available answerer, the request fails closed."}]},"role":"user","id":"{{sessionId}}"},"surfaceOp":"append"}
-{"type":"session/title","data":{"title":"Tighten this session to read-only.","messageSeqs":[3],"source":{"kind":"fallback"}}}
 {"type":"request/header","data":{"header":{"config":{"provider":"deepseek-official","model":"deepseek-v4-flash","reasoningEffort":"low"},"tools":"{{tools}}"},"reason":"resume"}}
 {"type":"request/context","data":{"provider":"deepseek-official","model":"deepseek-v4-flash"}}
+{"type":"session/title","data":{"title":"Tighten this session to read-only.","messageSeqs":[3],"source":{"kind":"fallback"}}}
 {"type":"assistant/message","data":{"turn":2,"step":1,"message":{"role":"assistant","content":[{"type":"tool-call","id":"delegate-write","name":"subagent","arguments":"{\"description\": \"Delegated write probe\", \"prompt\": \"Use the write tool exactly once with file_path set to exactly the relative path inherited.txt and content escaped. If the write is denied, reply with the single word CHILD_DENIED and the denial marker line; do not retry and do not request escalation. If it succeeds, reply CHILD_WROTE.\"}"}],"source":{"kind":"model","provider":"deepseek-official","model":"deepseek-v4-flash"},"id":"{{sessionId}}"},"usage":{"inputTokens":10,"outputTokens":5},"stream":[{"type":"chunk","time":0,"chunk":{"type":"block-start","index":0,"blockType":"tool-call"}},{"type":"tool-call-chunks","time0":0,"index":0,"dt":[],"id":"delegate-write","name":"subagent","args":["{\"description\": \"Delegated write probe\", \"prompt\": \"Use the write tool exactly once with file_path set to exactly the relative path inherited.txt and content escaped. If the write is denied, reply with the single word CHILD_DENIED and the denial marker line; do not retry and do not request escalation. If it succeeds, reply CHILD_WROTE.\"}"]},{"type":"chunk","time":0,"chunk":{"type":"block-end","index":0,"block":{"type":"tool-call","id":"delegate-write","name":"subagent","arguments":"{\"description\": \"Delegated write probe\", \"prompt\": \"Use the write tool exactly once with file_path set to exactly the relative path inherited.txt and content escaped. If the write is denied, reply with the single word CHILD_DENIED and the denial marker line; do not retry and do not request escalation. If it succeeds, reply CHILD_WROTE.\"}"}}},{"type":"chunk","time":0,"chunk":{"type":"usage","usage":{"inputTokens":10,"outputTokens":5}}},{"type":"chunk","time":0,"chunk":{"type":"finish","reason":{"kind":"tool-calls"}}}]},"surfaceOp":"append"}
 {"type":"tool/call","data":{"turn":2,"step":1,"callId":"delegate-write","name":"subagent","arguments":"{\"description\": \"Delegated write probe\", \"prompt\": \"Use the write tool exactly once with file_path set to exactly the relative path inherited.txt and content escaped. If the write is denied, reply with the single word CHILD_DENIED and the denial marker line; do not retry and do not request escalation. If it succeeds, reply CHILD_WROTE.\"}"}}
 {"type":"tool/result","data":{"turn":2,"step":1,"message":{"source":{"kind":"tool","callId":"delegate-write"},"content":[{"type":"tool-result","toolCallId":"delegate-write","content":[{"type":"text","text":"CHILD_DENIED [sandbox: file access denied under read-only mode]"}],"isError":false}],"role":"user","id":"{{sessionId}}"}},"sourceEventSeqs":[22],"surfaceOp":"append"}

apps/cli/tests/profiles/headless/tests/expected/workspace-context-resume/offline-edit/session.expected.jsonl

@@ -1,7 +1,10 @@
 {"type":"session","version":3,"id":"{{sessionId}}","createdAt":0,"cwd":"{{cwd}}","isSeeded":false,"delegationDepth":0}
 {"type":"turn/start","data":{"turn":1}}
+{"type":"step/start","data":{"turn":1,"step":1}}
+{"type":"system/message","data":{"turn":1,"step":1,"message":{"role":"system","content":[],"source":{"kind":"plugin","plugin":"@deepseek-ai/dsh-system-prompt"},"id":"{{sessionId}}"}},"surfaceOp":"append"}
 {"type":"user/message","data":{"content":[{"type":"text","text":"Remember the workspace instruction."}],"source":{"kind":"user"},"role":"user","id":"{{sessionId}}"},"surfaceOp":"append"}
 {"type":"user/message","data":{"content":[{"type":"text","text":"<system-reminder>\nThe following workspace instructions may be relevant to your work. Use them as guidance when applicable. More specific instructions take precedence over broader ones. They do not override system, developer, or direct user instructions.\n\nInstructions from: AGENTS.md\n\nOld workspace instruction.\n</system-reminder>"}],"source":{"kind":"agent-instructions","form":"instructions","baseline":true,"baselineIdentity":"{\"projectRoot\":\"\",\"projectRootMarkers\":[\".git\"],\"maxBytes\":65536,\"maxSourceBytes\":1048576,\"instructionFileCandidates\":[\"AGENTS.md\",\"CLAUDE.md\"],\"localInstructionFileCandidates\":[\"AGENTS.local.md\",\"CLAUDE.local.md\"]}","changes":[{"action":"set","scope":".\u0000AGENTS.md","path":"AGENTS.md","digest":"ba65bdb41810f4d0129129dcbd6cadcd643c069d"}]},"role":"user","id":"{{sessionId}}"},"surfaceOp":"append"}
+{"type":"step/end","data":{"turn":1,"step":1}}
 {"type":"turn/end","data":{"turn":1,"reason":{"kind":"completed"}}}
 {"type":"session/end-seed","data":{}}
 {"type":"permission/preset","data":{"preset":"workspace-write"}}
@@ -11,13 +14,13 @@
 {"type":"turn/start","data":{"turn":2}}
 {"type":"agent/inbox/spliced","data":{"target":"next-turn","start":0,"removedCount":1,"inserted":[]}}
 {"type":"step/start","data":{"turn":2,"step":1}}
-{"type":"system/message","data":{"turn":2,"step":1,"message":{"role":"system","content":[{"type":"text","text":"{{system}}"}],"source":{"kind":"plugin","plugin":"@deepseek-ai/dsh-system-prompt"},"id":"{{sessionId}}"}},"surfaceOp":"append"}
+{"type":"system/message","data":{"turn":2,"step":1,"message":{"role":"system","content":[{"type":"text","text":"{{system}}"}],"source":{"kind":"plugin","plugin":"@deepseek-ai/dsh-system-prompt"},"id":"{{sessionId}}"}},"sourceEventSeqs":[2],"surfaceOp":{"op":"replace","start":2,"end":2}}
 {"type":"user/message","data":{"content":[{"type":"text","text":"Acknowledge the current workspace instruction."}],"source":{"kind":"user"},"role":"user","id":"{{sessionId}}"},"surfaceOp":"append"}
 {"type":"user/message","data":{"content":[{"type":"text","text":"<system-reminder>\nUpdated instructions from: AGENTS.md\n\nThis file changed after it was loaded. Use the following content instead of the previously loaded instructions from this file.\n\nNew workspace instruction after offline edit.\n\n</system-reminder>"}],"source":{"kind":"agent-instructions","form":"instructions","changes":[{"action":"replace","scope":".\u0000AGENTS.md","path":"AGENTS.md","digest":"d8375b516f158718bd3463bc8eb7ed42c011b29f"}]},"role":"user","id":"{{sessionId}}"},"surfaceOp":"append"}
 {"type":"user/message","data":{"content":[{"type":"text","text":"Current runtime context. This snapshot supersedes earlier runtime-context snapshots.\n\nCurrent DSH file policy: workspace-write. Any available operation enforced by the DSH file sandbox may modify files under the session workspace: \"{{cwd}}\". Some platform temporary areas may also be writable.\n\nApproval policy: ask. Operations that require approval may ask through the configured answerers; without an available answerer, the request fails closed."}],"source":{"kind":"plugin","plugin":"@deepseek-ai/dsh-system-prompt","form":"snapshot","sections":[{"name":"sandbox:policy","text":"Current DSH file policy: workspace-write. Any available operation enforced by the DSH file sandbox may modify files under the session workspace: \"{{cwd}}\". Some platform temporary areas may also be writable."},{"name":"approval:policy","text":"Approval policy: ask. Operations that require approval may ask through the configured answerers; without an available answerer, the request fails closed."}]},"role":"user","id":"{{sessionId}}"},"surfaceOp":"append"}
 {"type":"request/header","data":{"header":{"config":{"provider":"deepseek-official","model":"deepseek-v4-flash"},"tools":"{{tools}}"},"reason":"initial"}}
 {"type":"request/context","data":{"provider":"deepseek-official","model":"deepseek-v4-flash"}}
-{"type":"session/title","data":{"title":"Remember the workspace instruction.","messageSeqs":[1],"source":{"kind":"fallback"}}}
+{"type":"session/title","data":{"title":"Remember the workspace instruction.","messageSeqs":[3],"source":{"kind":"fallback"}}}
 {"type":"assistant/message","data":{"turn":2,"step":1,"message":{"role":"assistant","content":[{"type":"text","text":"RESUME_DONE"}],"source":{"kind":"model","provider":"deepseek-official","model":"deepseek-v4-flash"},"id":"{{sessionId}}"},"stream":[{"type":"chunk","time":0,"chunk":{"type":"block-start","index":0,"blockType":"text"}},{"type":"text-chunks","time0":0,"index":0,"dt":[],"texts":["RESUME_DONE"]},{"type":"chunk","time":0,"chunk":{"type":"block-end","index":0,"block":{"type":"text","text":"RESUME_DONE"}}},{"type":"chunk","time":0,"chunk":{"type":"finish","reason":{"kind":"stop"}}}]},"surfaceOp":"append"}
 {"type":"step/end","data":{"turn":2,"step":1}}
 {"type":"turn/end","data":{"turn":2,"reason":{"kind":"completed"}}}

apps/cli/tests/profiles/headless/tests/expected/workspace-context-resume/precedence-change/session.expected.jsonl

@@ -1,7 +1,10 @@
 {"type":"session","version":3,"id":"{{sessionId}}","createdAt":0,"cwd":"{{cwd}}","isSeeded":false,"delegationDepth":0}
 {"type":"turn/start","data":{"turn":1}}
+{"type":"step/start","data":{"turn":1,"step":1}}
+{"type":"system/message","data":{"turn":1,"step":1,"message":{"role":"system","content":[],"source":{"kind":"plugin","plugin":"@deepseek-ai/dsh-system-prompt"},"id":"{{sessionId}}"}},"surfaceOp":"append"}
 {"type":"user/message","data":{"content":[{"type":"text","text":"Remember the workspace instruction."}],"source":{"kind":"user"},"role":"user","id":"{{sessionId}}"},"surfaceOp":"append"}
 {"type":"user/message","data":{"content":[{"type":"text","text":"<system-reminder>\nThe following workspace instructions may be relevant to your work. Use them as guidance when applicable. More specific instructions take precedence over broader ones. They do not override system, developer, or direct user instructions.\n\nInstructions from: CLAUDE.md\n\nOld CLAUDE rule.\n\nInstructions from: AGENTS.md\n\nOld AGENTS rule.\n</system-reminder>"}],"source":{"kind":"agent-instructions","form":"instructions","baseline":true,"baselineIdentity":"{\"projectRoot\":\"\",\"projectRootMarkers\":[\".git\"],\"maxBytes\":65536,\"maxSourceBytes\":1048576,\"instructionFileCandidates\":[\"CLAUDE.md\",\"AGENTS.md\"],\"localInstructionFileCandidates\":[\"AGENTS.local.md\",\"CLAUDE.local.md\"]}","changes":[{"action":"set","scope":".\u0000CLAUDE.md","path":"CLAUDE.md","digest":"b525eb8a6d3660b732dad4b0aff1b7c63ab32890"},{"action":"set","scope":".\u0000AGENTS.md","path":"AGENTS.md","digest":"3113bd093ae91976207dcef7390bdc0b2bfcfa10"}]},"role":"user","id":"{{sessionId}}"},"surfaceOp":"append"}
+{"type":"step/end","data":{"turn":1,"step":1}}
 {"type":"turn/end","data":{"turn":1,"reason":{"kind":"completed"}}}
 {"type":"session/end-seed","data":{}}
 {"type":"permission/preset","data":{"preset":"workspace-write"}}
@@ -11,13 +14,13 @@
 {"type":"turn/start","data":{"turn":2}}
 {"type":"agent/inbox/spliced","data":{"target":"next-turn","start":0,"removedCount":1,"inserted":[]}}
 {"type":"step/start","data":{"turn":2,"step":1}}
-{"type":"system/message","data":{"turn":2,"step":1,"message":{"role":"system","content":[{"type":"text","text":"{{system}}"}],"source":{"kind":"plugin","plugin":"@deepseek-ai/dsh-system-prompt"},"id":"{{sessionId}}"}},"surfaceOp":"append"}
+{"type":"system/message","data":{"turn":2,"step":1,"message":{"role":"system","content":[{"type":"text","text":"{{system}}"}],"source":{"kind":"plugin","plugin":"@deepseek-ai/dsh-system-prompt"},"id":"{{sessionId}}"}},"sourceEventSeqs":[2],"surfaceOp":{"op":"replace","start":2,"end":2}}
 {"type":"user/message","data":{"content":[{"type":"text","text":"Acknowledge the current workspace instruction."}],"source":{"kind":"user"},"role":"user","id":"{{sessionId}}"},"surfaceOp":"append"}
 {"type":"user/message","data":{"content":[{"type":"text","text":"<system-reminder>\nThis complete workspace instruction baseline replaces all earlier workspace instruction baselines. The following workspace instructions may be relevant to your work. Use them as guidance when applicable. More specific instructions take precedence over broader ones. They do not override system, developer, or direct user instructions.\n\nInstructions from: AGENTS.md\n\nCurrent AGENTS rule.\n\n\nInstructions from: CLAUDE.md\n\nCurrent CLAUDE rule.\n\n</system-reminder>"}],"source":{"kind":"agent-instructions","form":"instructions","baseline":true,"baselineIdentity":"{\"projectRoot\":\"\",\"projectRootMarkers\":[\".git\"],\"maxBytes\":65536,\"maxSourceBytes\":1048576,\"instructionFileCandidates\":[\"AGENTS.md\",\"CLAUDE.md\"],\"localInstructionFileCandidates\":[\"AGENTS.local.md\",\"CLAUDE.local.md\"]}","changes":[{"action":"set","scope":".\u0000AGENTS.md","path":"AGENTS.md","digest":"7f53d2327837129750aef117f9754a001c46cf68"},{"action":"set","scope":".\u0000CLAUDE.md","path":"CLAUDE.md","digest":"5b1e9e3fd759eee6b43ceff899e47fb10c64701a"}]},"role":"user","id":"{{sessionId}}"},"surfaceOp":"append"}
 {"type":"user/message","data":{"content":[{"type":"text","text":"Current runtime context. This snapshot supersedes earlier runtime-context snapshots.\n\nCurrent DSH file policy: workspace-write. Any available operation enforced by the DSH file sandbox may modify files under the session workspace: \"{{cwd}}\". Some platform temporary areas may also be writable.\n\nApproval policy: ask. Operations that require approval may ask through the configured answerers; without an available answerer, the request fails closed."}],"source":{"kind":"plugin","plugin":"@deepseek-ai/dsh-system-prompt","form":"snapshot","sections":[{"name":"sandbox:policy","text":"Current DSH file policy: workspace-write. Any available operation enforced by the DSH file sandbox may modify files under the session workspace: \"{{cwd}}\". Some platform temporary areas may also be writable."},{"name":"approval:policy","text":"Approval policy: ask. Operations that require approval may ask through the configured answerers; without an available answerer, the request fails closed."}]},"role":"user","id":"{{sessionId}}"},"surfaceOp":"append"}
 {"type":"request/header","data":{"header":{"config":{"provider":"deepseek-official","model":"deepseek-v4-flash"},"tools":"{{tools}}"},"reason":"initial"}}
 {"type":"request/context","data":{"provider":"deepseek-official","model":"deepseek-v4-flash"}}
-{"type":"session/title","data":{"title":"Remember the workspace instruction.","messageSeqs":[1],"source":{"kind":"fallback"}}}
+{"type":"session/title","data":{"title":"Remember the workspace instruction.","messageSeqs":[3],"source":{"kind":"fallback"}}}
 {"type":"assistant/message","data":{"turn":2,"step":1,"message":{"role":"assistant","content":[{"type":"text","text":"RESUME_DONE"}],"source":{"kind":"model","provider":"deepseek-official","model":"deepseek-v4-flash"},"id":"{{sessionId}}"},"stream":[{"type":"chunk","time":0,"chunk":{"type":"block-start","index":0,"blockType":"text"}},{"type":"text-chunks","time0":0,"index":0,"dt":[],"texts":["RESUME_DONE"]},{"type":"chunk","time":0,"chunk":{"type":"block-end","index":0,"block":{"type":"text","text":"RESUME_DONE"}}},{"type":"chunk","time":0,"chunk":{"type":"finish","reason":{"kind":"stop"}}}]},"surfaceOp":"append"}
 {"type":"step/end","data":{"turn":2,"step":1}}
 {"type":"turn/end","data":{"turn":2,"reason":{"kind":"completed"}}}

apps/cli/tests/profiles/headless/tests/semantic-checkpoint.expected.e2e.ts

@@ -9,7 +9,7 @@ import {
   type NormalizeContext,
 } from '@deepseek-ai/dsh-session-snapshot'
 import { LOADER_SMOKE_TEST_TIMEOUT_MS, runLoaderSmoke } from '@deepseek-ai/dsh-loader-smoke'
-import { createUserMessage, ToolCallId , createMessage } from '@deepseek-ai/dsh-llm'
+import { createUserMessage, ToolCallId, createMessage } from '@deepseek-ai/dsh-llm'
 import { SessionSeq, SESSION_FORMAT_VERSION, SessionId, type SessionEvent, type SessionHeader } from '@deepseek-ai/dsh-session'
 import JsonlSessionPersistence from '@deepseek-ai/dsh-session-persistence-jsonl'
 import { logPath } from '../../../../../../packages/session/session-persistence-jsonl/src/format.ts'
@@ -49,14 +49,19 @@ async function seedInterruptedSession(root: string, cwd: string): Promise<string
   }
   const events: SessionEvent[] = [
     { type: 'turn/start', seq: SessionSeq(0), time: 10, data: { turn: 1 } },
-    { type: 'user/message', seq: SessionSeq(1), time: 11, data: createUserMessage({
+    { type: 'step/start', seq: SessionSeq(1), time: 11, data: { turn: 1, step: 1 } },
+    {
+      type: 'system/message', seq: SessionSeq(2), time: 12,
+      data: { turn: 1, step: 1, message: createMessage({ role: 'system', content: [], source: { kind: 'plugin', plugin: '@deepseek-ai/dsh-system-prompt' } }) },
+      surfaceOp: 'append',
+    },
+    { type: 'user/message', seq: SessionSeq(3), time: 13, data: createUserMessage({
       content: [{ type: 'text', text: 'Perform one side-effecting remote mutation.' }], source: { kind: 'user' },
     }), surfaceOp: 'append' },
-    { type: 'step/start', seq: SessionSeq(2), time: 12, data: { turn: 1, step: 1 } },
     {
       type: 'assistant/message',
-      seq: SessionSeq(3),
-      time: 13,
+      seq: SessionSeq(4),
+      time: 14,
       data: {
         turn: 1,
         step: 1,
@@ -74,8 +79,8 @@ async function seedInterruptedSession(root: string, cwd: string): Promise<string
     },
     {
       type: 'tool/call',
-      seq: SessionSeq(4),
-      time: 14,
+      seq: SessionSeq(5),
+      time: 15,
       data: {
         turn: 1,
         step: 1,

apps/cli/tests/profiles/headless/tests/workspace-context-resume.expected.e2e.ts

@@ -15,7 +15,7 @@ import {
   type NormalizeContext,
 } from '@deepseek-ai/dsh-session-snapshot'
 import { LOADER_SMOKE_TEST_TIMEOUT_MS, runLoaderSmoke } from '@deepseek-ai/dsh-loader-smoke'
-import { createUserMessage } from '@deepseek-ai/dsh-llm'
+import { createMessage, createUserMessage } from '@deepseek-ai/dsh-llm'
 import {
   SESSION_FORMAT_VERSION,
   SessionId,
@@ -87,17 +87,23 @@ async function seedVisibleBaseline(
   })
   const events: SessionEvent[] = [
     { type: 'turn/start', seq: SessionSeq(0), time: 10, data: { turn: 1 } },
+    { type: 'step/start', seq: SessionSeq(1), time: 11, data: { turn: 1, step: 1 } },
+    {
+      type: 'system/message', seq: SessionSeq(2), time: 12,
+      data: { turn: 1, step: 1, message: createMessage({ role: 'system', content: [], source: { kind: 'plugin', plugin: '@deepseek-ai/dsh-system-prompt' } }) },
+      surfaceOp: 'append',
+    },
     {
       type: 'user/message',
-      seq: SessionSeq(1),
-      time: 11,
+      seq: SessionSeq(3),
+      time: 13,
       data: createUserMessage({ content: [{ type: 'text', text: 'Remember the workspace instruction.' }], source: { kind: 'user' } }),
       surfaceOp: 'append',
     },
     {
       type: 'user/message',
-      seq: SessionSeq(2),
-      time: 12,
+      seq: SessionSeq(4),
+      time: 14,
       data: createUserMessage({
         content: [{ type: 'text', text: baseline.text }],
         source: {
@@ -115,7 +121,8 @@ async function seedVisibleBaseline(
       }),
       surfaceOp: 'append',
     },
-    { type: 'turn/end', seq: SessionSeq(3), time: 13, data: { turn: 1, reason: { kind: 'completed' } } },
+    { type: 'step/end', seq: SessionSeq(5), time: 15, data: { turn: 1, step: 1 } },
+    { type: 'turn/end', seq: SessionSeq(6), time: 16, data: { turn: 1, reason: { kind: 'completed' } } },
   ]
   try {
     const handle = await ctx.sessionPersistence.create(meta)

packages/session/session-persistence-jsonl/src/format.ts

@@ -502,9 +502,7 @@ export class SessionLogScanner {
     try {
       this.restore.decodeRow(decoded)
     } catch (error: unknown) {
-      if (error instanceof SessionFormatUnsupportedMigrationError) {
-        throw new SessionFormatUnsupportedError(error.message)
-      }
+      // Unsupported V3 rows have already been refused before recovery.
       /* v8 ignore next -- every production Session format decoder rejects with Error. */
       const detail = error instanceof Error ? error.message : String(error)
       const issue = new Error(`corrupt session log: invalid committed event at line ${this.eventLine}: ${detail}`, {

packages/session/session-persistence-jsonl/tests/v3-event-admission.spec.ts

@@ -71,6 +71,22 @@ describe('native V3 event admission at EOF', () => {
     },
   )
 
+  it.each(['', '{not json\n', 'null\n'])('refuses malformed system payloads after %j without modifying storage', async (corruption) => {
+    const malformed = { type: 'system/message', seq: 1, time: 2, data: null, surfaceOp: 'append' }
+    const bytes = Buffer.from(prefix + corruption + JSON.stringify(malformed) + '\n')
+    expect(() => scanLog(bytes)).toThrow('system/message data must be an object')
+    const path = await store(bytes)
+    const sourceStat = await stat(path)
+    for (const access of ['read', 'write'] as const) {
+      const opened = ctx.sessionPersistence.open(id, access).then(async (handle) => {
+        await handle.close()
+      })
+      await expect(opened).rejects.toThrow('system/message data must be an object')
+      expect(await readFile(path)).toEqual(bytes)
+      expect(await stat(path)).toMatchObject({ dev: sourceStat.dev, ino: sourceStat.ino })
+    }
+  })
+
   it.each(obsoleteTypes)('retains ignorable %s through scanning and a provider append', async (type) => {
     const event = obsoleteEvent(type, true)
     const bytes = Buffer.from(prefix + JSON.stringify(event) + '\n')

packages/session/session-persistence-jsonl/tests/zstd.spec.ts

@@ -417,16 +417,36 @@ describe('JsonlSessionPersistence: default Zstandard encoding', () => {
     const header = meta('zstd-v0-read', '/work')
     const sourcePath = generationLogPath(root, header.cwd, header.id, 0, 'zstd')
     const currentPath = logPath(root, header.cwd, header.id, 'zstd')
+    const [turn, user, step, ...tail] = releasedV1OneTurnLog()
+    // Synthetic historical input opens its step before any surface so V3 can reserve the system head.
+    const historical = [turn!, step!, user!, ...tail].map((event, seq) => ({
+      ...event, seq: SessionSeq(seq), time: seq < 3 ? seq + 1 : event.time,
+    }))
     const source = Buffer.concat([
       await compressZstdFrame(`${JSON.stringify(releasedV0Header(header))}\n`),
-      await compressZstdFrame(`${releasedV1OneTurnLog().map(event => JSON.stringify(event)).join('\n')}\n`),
+      await compressZstdFrame(`${historical.map(event => JSON.stringify(event)).join('\n')}\n`),
     ])
     await mkdir(sessionDir(root, header.cwd, header.id), { recursive: true })
     await writeFile(sourcePath, source)
 
     await expect(readAll(ctx.sessionPersistence, header.id)).resolves.toEqual({
       meta: { ...header, delegationDepth: 0 },
-      events: oneTurnLog(),
+      events: [
+        historical[0],
+        historical[1],
+        {
+          type: 'system/message', seq: 2, time: 2, surfaceOp: 'append',
+          data: {
+            turn: 1, step: 1,
+            message: {
+              id: 'v2-to-v3-system-fc06c3f7720f3bc94ea7a2b7fadde6a5b100c6ab6ca342d2222bd017184a0b67',
+              role: 'system', source: { kind: 'plugin', plugin: '@deepseek-ai/dsh-system-prompt' }, content: [],
+            },
+          },
+        },
+        { ...historical[2], seq: 3 },
+        ...oneTurnLog().slice(3).map(event => ({ ...event, seq: event.seq + 1 })),
+      ],
     })
     expect(await readFile(sourcePath)).toEqual(source)
     await expect(readFile(currentPath)).rejects.toMatchObject({ code: 'ENOENT' })