eyeling 1.24.7 → 1.24.9

package/examples/output/{act-alarm-bit-interoperability.txt → act-alarm-bit-interoperability.md}

@@ -1,20 +1,26 @@
-ACT harbor alarm bit interoperability
+# act-alarm-bit-interoperability  
 
-Answer
-YES for the classical alarm bit.
-NO for universal cloning and unrestricted fan-out of the quantum-like token.
+## Source files  
 
-Reason Why
-The alarm state is modeled as an abstract bit carried by two unlike classical substrates. Because both the optical beacon and the relay register are information media for the same variable, local permutation and copying in both directions are possible. By contrast, the quantum-like token is treated as a superinformation medium, so universal cloning of all of its states is impossible, and unrestricted classical-style fan-out is blocked as well.
+- [N3 rules](../act-alarm-bit-interoperability.n3)  
 
-Check
-C1  OK - the optical beacon is an information medium
-C2  OK - the relay register is an information medium
-C3  OK - both substrates encode the same abstract variable: AlarmBit
-C4  OK - AlarmBit can be copied from optical beacon to relay register
-C5  OK - AlarmBit can be copied from relay register to optical beacon
-C6  OK - local permutation of AlarmBit is possible on the optical beacon
-C7  OK - local permutation of AlarmBit is possible on the relay register
-C8  OK - cloning all states of the quantum token is an impossible task
-C9  OK - the quantum token cannot be universally cloned
-C10 OK - the quantum token cannot support unrestricted classical-style fan-out
+ACT harbor alarm bit interoperability  
+
+## Answer  
+YES for the classical alarm bit.  
+NO for universal cloning and unrestricted fan-out of the quantum-like token.  
+
+## Reason Why  
+The alarm state is modeled as an abstract bit carried by two unlike classical substrates. Because both the optical beacon and the relay register are information media for the same variable, local permutation and copying in both directions are possible. By contrast, the quantum-like token is treated as a superinformation medium, so universal cloning of all of its states is impossible, and unrestricted classical-style fan-out is blocked as well.  
+
+## Check  
+C1  OK - the optical beacon is an information medium  
+C2  OK - the relay register is an information medium  
+C3  OK - both substrates encode the same abstract variable: AlarmBit  
+C4  OK - AlarmBit can be copied from optical beacon to relay register  
+C5  OK - AlarmBit can be copied from relay register to optical beacon  
+C6  OK - local permutation of AlarmBit is possible on the optical beacon  
+C7  OK - local permutation of AlarmBit is possible on the relay register  
+C8  OK - cloning all states of the quantum token is an impossible task  
+C9  OK - the quantum token cannot be universally cloned  
+C10 OK - the quantum token cannot support unrestricted classical-style fan-out  

package/examples/output/act-barley-seed-lineage.md

@@ -0,0 +1,31 @@
+# act-barley-seed-lineage  
+
+## Source files  
+
+- [N3 rules](../act-barley-seed-lineage.n3)  
+
+ACT barley seed lineage — can and can't  
+
+## Answer  
+YES for the viable barley lineage.  
+NO for the contrast lineages when digital heredity, repair, protected dormancy, or heritable variation are missing.  
+
+## Reason Why  
+The main lineage can achieve genome copying under no-design laws because its hereditary information is digitally instantiated. It can also pass through protected dormancy, germinate, produce propagules, reproduce accurately, close its life cycle, and adaptively persist under saline selection. But the contrast lineages show the "can't" side: non-digital heredity blocks accurate genome copying under no-design laws, lack of repair blocks accurate self-reproduction, lack of dormancy protection blocks lineage closure through a protected seed phase, and lack of heritable variation blocks adaptive evolution and thus blocks evolvability.  
+
+## Check  
+C1  OK - no-design laws are assumed  
+C2  OK - the viable genome can be copied under no-design laws  
+C3  OK - the viable seed can achieve protected dormancy  
+C4  OK - the viable seed can germinate  
+C5  OK - the viable adult can produce propagules  
+C6  OK - the viable lineage can achieve accurate self-reproduction  
+C7  OK - the viable lineage can achieve lineage closure  
+C8  OK - the viable lineage can exhibit heritable variation  
+C9  OK - the viable lineage can adaptively persist  
+C10 OK - the viable lineage is evolvable  
+C11 OK - the non-digital lineage cannot achieve accurate self-reproduction  
+C12 OK - the repair-deficient lineage cannot achieve accurate self-reproduction  
+C13 OK - the coatless lineage cannot achieve lineage closure through protected dormancy  
+C14 OK - the static lineage cannot achieve adaptive evolution  
+C15 OK - the static lineage cannot be an evolvable lineage  

package/examples/output/{act-docking-abort.txt → act-docking-abort.md}

@@ -1,22 +1,28 @@
-ACT docking abort token — constructor-theory coverage case
+# act-docking-abort  
 
-Answer
-YES for the classical abort token.
-NO for universal cloning and unrestricted audit fan-out of the quantum seal.
+## Source files  
 
-Reason Why
-The docking-abort token is treated as an abstract information variable carried by unlike classical media: lamp state, PLC register, radio frame, and audit display. Because those substrates are information media for the same variable, the token can be permuted locally, cloned locally, copied across media, measured into an output record, and embedded in serial and parallel task networks. By contrast, the quantum authenticity seal is treated as a superinformation medium, so cloning all of its states is impossible and unrestricted audit fan-out is blocked.
+- [N3 rules](../act-docking-abort.n3)  
 
-Check
-C1  OK - the abort lamp is a computation medium
-C2  OK - the abort lamp distinguishes the abort bit
-C3  OK - permutation of the abort bit is possible on the abort lamp
-C4  OK - local cloning of the abort bit is possible on the PLC register
-C5  OK - the abort bit can be copied from lamp to PLC
-C6  OK - the abort bit can be copied from PLC to radio frame
-C7  OK - the abort bit can be measured from radio frame into the audit display
-C8  OK - a serial network from lamp via PLC to audit display is possible
-C9  OK - a parallel network from PLC to radio frame and audit display is possible
-C10 OK - cloning all states of the quantum seal is an impossible task
-C11 OK - the quantum seal cannot be universally cloned
-C12 OK - the quantum seal cannot be used for unrestricted audit fan-out
+ACT docking abort token — constructor-theory coverage case  
+
+## Answer  
+YES for the classical abort token.  
+NO for universal cloning and unrestricted audit fan-out of the quantum seal.  
+
+## Reason Why  
+The docking-abort token is treated as an abstract information variable carried by unlike classical media: lamp state, PLC register, radio frame, and audit display. Because those substrates are information media for the same variable, the token can be permuted locally, cloned locally, copied across media, measured into an output record, and embedded in serial and parallel task networks. By contrast, the quantum authenticity seal is treated as a superinformation medium, so cloning all of its states is impossible and unrestricted audit fan-out is blocked.  
+
+## Check  
+C1  OK - the abort lamp is a computation medium  
+C2  OK - the abort lamp distinguishes the abort bit  
+C3  OK - permutation of the abort bit is possible on the abort lamp  
+C4  OK - local cloning of the abort bit is possible on the PLC register  
+C5  OK - the abort bit can be copied from lamp to PLC  
+C6  OK - the abort bit can be copied from PLC to radio frame  
+C7  OK - the abort bit can be measured from radio frame into the audit display  
+C8  OK - a serial network from lamp via PLC to audit display is possible  
+C9  OK - a parallel network from PLC to radio frame and audit display is possible  
+C10 OK - cloning all states of the quantum seal is an impossible task  
+C11 OK - the quantum seal cannot be universally cloned  
+C12 OK - the quantum seal cannot be used for unrestricted audit fan-out  

package/examples/output/{act-gravity-mediator-witness.txt → act-gravity-mediator-witness.md}

@@ -1,24 +1,30 @@
-ACT gravity mediator witness
+# act-gravity-mediator-witness  
 
-Answer
-YES for the mediator-only witness run.
-NO for a purely classical mediator model under the same mediator-only conditions.
+## Source files  
 
-Reason Why
-The positive run assumes locality and interoperability, excludes direct coupling between the two quantum systems, and records an entanglement witness after interaction through the mediator alone. Under those constructor-theoretic conditions, the mediator must be non-classical, so the run rules out a purely classical mediator model. The contrast run keeps the same locality, interoperability, and mediator-only structure but assigns the mediator a purely classical model. In that case the mediator-only entanglement witness is blocked, so the run cannot support the same non-classicality conclusion.
+- [N3 rules](../act-gravity-mediator-witness.n3)  
 
-Check
-C1  OK - locality is assumed in the positive run
-C2  OK - interoperability is assumed in the positive run
-C3  OK - direct coupling between the two quantum systems is excluded
-C4  OK - the positive run has a mediator-only interaction path
-C5  OK - an entanglement witness is observed in the positive run
-C6  OK - the positive run supports an information-transfer interface
-C7  OK - the positive run supports local readout
-C8  OK - the positive mediator is derived to be non-classical
-C9  OK - a purely classical mediator model is ruled out by the positive run
-C10 OK - the non-classicality conclusion applies to the gravitational mediator
-C11 OK - the contrast run is also mediator-only
-C12 OK - the contrast run cannot support a mediator-only entanglement witness
-C13 OK - the purely classical gravitational mediator cannot mediate entanglement under the witness conditions
-C14 OK - the contrast run cannot support the non-classicality conclusion
+ACT gravity mediator witness  
+
+## Answer  
+YES for the mediator-only witness run.  
+NO for a purely classical mediator model under the same mediator-only conditions.  
+
+## Reason Why  
+The positive run assumes locality and interoperability, excludes direct coupling between the two quantum systems, and records an entanglement witness after interaction through the mediator alone. Under those constructor-theoretic conditions, the mediator must be non-classical, so the run rules out a purely classical mediator model. The contrast run keeps the same locality, interoperability, and mediator-only structure but assigns the mediator a purely classical model. In that case the mediator-only entanglement witness is blocked, so the run cannot support the same non-classicality conclusion.  
+
+## Check  
+C1  OK - locality is assumed in the positive run  
+C2  OK - interoperability is assumed in the positive run  
+C3  OK - direct coupling between the two quantum systems is excluded  
+C4  OK - the positive run has a mediator-only interaction path  
+C5  OK - an entanglement witness is observed in the positive run  
+C6  OK - the positive run supports an information-transfer interface  
+C7  OK - the positive run supports local readout  
+C8  OK - the positive mediator is derived to be non-classical  
+C9  OK - a purely classical mediator model is ruled out by the positive run  
+C10 OK - the non-classicality conclusion applies to the gravitational mediator  
+C11 OK - the contrast run is also mediator-only  
+C12 OK - the contrast run cannot support a mediator-only entanglement witness  
+C13 OK - the purely classical gravitational mediator cannot mediate entanglement under the witness conditions  
+C14 OK - the contrast run cannot support the non-classicality conclusion  

package/examples/output/{act-isolation-breach.txt → act-isolation-breach.md}

@@ -1,27 +1,33 @@
-ACT isolation-breach token — broad constructor-theory coverage case
+# act-isolation-breach  
 
-Answer
-YES for the classical isolation-breach token.
-NO for universal cloning and unrestricted fan-out of the quantum provenance seal.
+## Source files  
 
-Reason Why
-The isolation-breach token is treated as an abstract information variable carried by unlike classical media: a door beacon, a containment PLC, a nurse pager, and an incident board. Because those substrates are information media for the same variable, the token can be prepared, permuted, reversed, cloned locally, copied across media, measured into an output record, and composed into serial and parallel task networks. By contrast, the specimen seal is treated as a superinformation medium, so cloning all of its states is impossible and unrestricted parallel fan-out is blocked.
+- [N3 rules](../act-isolation-breach.n3)  
 
-Check
-C1  OK - the door beacon is an information medium
-C2  OK - the containment PLC is an information medium
-C3  OK - the nurse pager is an information medium
-C4  OK - the incident board is an information medium
-C5  OK - the door beacon distinguishes the breach bit
-C6  OK - the breach state can be prepared on the nurse pager
-C7  OK - permutation from safe to breach is possible on the door beacon
-C8  OK - the door beacon supports reversible permutation
-C9  OK - local cloning of the breach bit is possible on the containment PLC
-C10 OK - the breach bit can be copied from door beacon to containment PLC
-C11 OK - the breach bit can be copied from containment PLC to nurse pager
-C12 OK - the breach bit can be measured from nurse pager into the incident board
-C13 OK - a serial network from door beacon via containment PLC to incident board is possible
-C14 OK - a parallel network from containment PLC to nurse pager and incident board is possible
-C15 OK - cloning all states of the specimen seal is an impossible task
-C16 OK - the specimen seal cannot be universally cloned
-C17 OK - the specimen seal cannot support unrestricted parallel fan-out
+ACT isolation-breach token — broad constructor-theory coverage case  
+
+## Answer  
+YES for the classical isolation-breach token.  
+NO for universal cloning and unrestricted fan-out of the quantum provenance seal.  
+
+## Reason Why  
+The isolation-breach token is treated as an abstract information variable carried by unlike classical media: a door beacon, a containment PLC, a nurse pager, and an incident board. Because those substrates are information media for the same variable, the token can be prepared, permuted, reversed, cloned locally, copied across media, measured into an output record, and composed into serial and parallel task networks. By contrast, the specimen seal is treated as a superinformation medium, so cloning all of its states is impossible and unrestricted parallel fan-out is blocked.  
+
+## Check  
+C1  OK - the door beacon is an information medium  
+C2  OK - the containment PLC is an information medium  
+C3  OK - the nurse pager is an information medium  
+C4  OK - the incident board is an information medium  
+C5  OK - the door beacon distinguishes the breach bit  
+C6  OK - the breach state can be prepared on the nurse pager  
+C7  OK - permutation from safe to breach is possible on the door beacon  
+C8  OK - the door beacon supports reversible permutation  
+C9  OK - local cloning of the breach bit is possible on the containment PLC  
+C10 OK - the breach bit can be copied from door beacon to containment PLC  
+C11 OK - the breach bit can be copied from containment PLC to nurse pager  
+C12 OK - the breach bit can be measured from nurse pager into the incident board  
+C13 OK - a serial network from door beacon via containment PLC to incident board is possible  
+C14 OK - a parallel network from containment PLC to nurse pager and incident board is possible  
+C15 OK - cloning all states of the specimen seal is an impossible task  
+C16 OK - the specimen seal cannot be universally cloned  
+C17 OK - the specimen seal cannot support unrestricted parallel fan-out  

package/examples/output/{act-photosynthetic-exciton-transfer.txt → act-photosynthetic-exciton-transfer.md}

@@ -1,20 +1,26 @@
-ACT photosynthetic exciton transfer
+# act-photosynthetic-exciton-transfer  
 
-Answer
-YES for the tuned antenna complex.
-NO for the detuned, strongly decohered contrast complex.
+## Source files  
 
-Reason Why
-The tuned complex can sample exciton pathways coherently, use vibronically assisted transfer, and exploit short-lived quantum assistance along a downhill route to the reaction center. That makes efficient exciton transfer and reaction-center delivery possible in this case. The detuned contrast complex lacks the same alignment: coherent pathway sampling is blocked, vibronic assistance is unavailable, and the energy landscape is mismatched, so efficient reaction-center delivery is not possible in the same operating picture.
+- [N3 rules](../act-photosynthetic-exciton-transfer.n3)  
 
-Check
-C1  OK - the tuned complex can sample exciton pathways coherently
-C2  OK - the tuned complex can use vibronically assisted transfer
-C3  OK - short-lived quantum assistance is enough in the tuned downhill regime
-C4  OK - efficient exciton transfer is possible in the tuned complex
-C5  OK - the tuned complex can deliver excitation to the reaction center
-C6  OK - the detuned complex cannot sample pathways coherently
-C7  OK - the detuned complex cannot use vibronically assisted transfer
-C8  OK - the detuned complex cannot achieve directed reaction-center transfer
-C9  OK - the detuned complex cannot achieve efficient exciton transfer
-C10 OK - the detuned complex cannot deliver excitation efficiently to the reaction center
+ACT photosynthetic exciton transfer  
+
+## Answer  
+YES for the tuned antenna complex.  
+NO for the detuned, strongly decohered contrast complex.  
+
+## Reason Why  
+The tuned complex can sample exciton pathways coherently, use vibronically assisted transfer, and exploit short-lived quantum assistance along a downhill route to the reaction center. That makes efficient exciton transfer and reaction-center delivery possible in this case. The detuned contrast complex lacks the same alignment: coherent pathway sampling is blocked, vibronic assistance is unavailable, and the energy landscape is mismatched, so efficient reaction-center delivery is not possible in the same operating picture.  
+
+## Check  
+C1  OK - the tuned complex can sample exciton pathways coherently  
+C2  OK - the tuned complex can use vibronically assisted transfer  
+C3  OK - short-lived quantum assistance is enough in the tuned downhill regime  
+C4  OK - efficient exciton transfer is possible in the tuned complex  
+C5  OK - the tuned complex can deliver excitation to the reaction center  
+C6  OK - the detuned complex cannot sample pathways coherently  
+C7  OK - the detuned complex cannot use vibronically assisted transfer  
+C8  OK - the detuned complex cannot achieve directed reaction-center transfer  
+C9  OK - the detuned complex cannot achieve efficient exciton transfer  
+C10 OK - the detuned complex cannot deliver excitation efficiently to the reaction center  

package/examples/output/{act-sensor-memory-reset.txt → act-sensor-memory-reset.md}

@@ -1,20 +1,26 @@
-ACT sensor memory reset
+# act-sensor-memory-reset  
 
-Answer
-YES with the battery pack.
-NO with the ambient heat bath alone.
+## Source files  
 
-Reason Why
-The alarm latch is a one-bit memory that must be reset to its standard clear state before the radiation sensor can be reused. In this case, the charged battery pack is treated as a work medium, so it can drive a controlled reset and prepare the latch in its reusable standard state. The ambient bath is treated as a heat medium, so by itself it cannot perform the same reliable directed reset. The example also shows an irreversibility pattern: useful work can be degraded into dissipated heat during reset, but the ambient heat bath alone cannot reconstruct the charged work resource.
+- [N3 rules](../act-sensor-memory-reset.n3)  
 
-Check
-C1  OK - the battery pack can drive a controlled reset
-C2  OK - the alarm latch can be reliably reset from work
-C3  OK - the latch can be prepared in its standard reusable state
-C4  OK - the sensor can be made ready for reuse
-C5  OK - the work resource can degrade to heat during reset
-C6  OK - the ambient heat bath cannot drive a controlled reset
-C7  OK - the latch cannot be reliably reset from heat alone
-C8  OK - the latch cannot be prepared in its standard state from heat alone
-C9  OK - the sensor cannot be made ready for reuse from heat alone
-C10 OK - the ambient heat bath cannot reconstruct the charged work resource by itself
+ACT sensor memory reset  
+
+## Answer  
+YES with the battery pack.  
+NO with the ambient heat bath alone.  
+
+## Reason Why  
+The alarm latch is a one-bit memory that must be reset to its standard clear state before the radiation sensor can be reused. In this case, the charged battery pack is treated as a work medium, so it can drive a controlled reset and prepare the latch in its reusable standard state. The ambient bath is treated as a heat medium, so by itself it cannot perform the same reliable directed reset. The example also shows an irreversibility pattern: useful work can be degraded into dissipated heat during reset, but the ambient heat bath alone cannot reconstruct the charged work resource.  
+
+## Check  
+C1  OK - the battery pack can drive a controlled reset  
+C2  OK - the alarm latch can be reliably reset from work  
+C3  OK - the latch can be prepared in its standard reusable state  
+C4  OK - the sensor can be made ready for reuse  
+C5  OK - the work resource can degrade to heat during reset  
+C6  OK - the ambient heat bath cannot drive a controlled reset  
+C7  OK - the latch cannot be reliably reset from heat alone  
+C8  OK - the latch cannot be prepared in its standard state from heat alone  
+C9  OK - the sensor cannot be made ready for reuse from heat alone  
+C10 OK - the ambient heat bath cannot reconstruct the charged work resource by itself  

package/examples/output/{act-tunnel-junction-wake-switch.txt → act-tunnel-junction-wake-switch.md}

@@ -1,21 +1,27 @@
-ACT tunnel-junction wake switch
+# act-tunnel-junction-wake-switch  
 
-Answer
-YES for the tunnel junction.
-NO for the conventional low-bias PN junction in the same wake-switch regime.
+## Source files  
 
-Reason Why
-The tunnel junction is modeled as a heavily doped narrow PN junction with overlapping states, so quantum barrier transfer is possible. That makes sub-threshold current possible in the low-forward-bias regime, which in turn makes ultra-low-bias switching possible for the wake circuit. Because the device is also scanned through a peak-to-valley window, a negative differential response is possible as well. By contrast, the conventional junction lacks the structural conditions for the same transfer mode, so it cannot deliver the same low-bias switching task in this case.
+- [N3 rules](../act-tunnel-junction-wake-switch.n3)  
 
-Check
-C1  OK - the tunnel junction can support quantum barrier transfer
-C2  OK - the tunnel junction is classified as tunneling-dominant
-C3  OK - the tunnel junction can deliver sub-threshold current
-C4  OK - the tunnel junction can show negative differential response
-C5  OK - the tunnel junction can perform ultra-low-bias switching
-C6  OK - the tunnel junction can serve the leak-alarm wake circuit
-C7  OK - the conventional junction cannot support the same quantum barrier transfer
-C8  OK - the conventional junction cannot deliver sub-threshold current in this regime
-C9  OK - the conventional junction cannot show the tunnel-style negative differential response
-C10 OK - the conventional junction cannot perform ultra-low-bias switching here
-C11 OK - the conventional junction cannot serve the leak-alarm wake circuit in this case
+ACT tunnel-junction wake switch  
+
+## Answer  
+YES for the tunnel junction.  
+NO for the conventional low-bias PN junction in the same wake-switch regime.  
+
+## Reason Why  
+The tunnel junction is modeled as a heavily doped narrow PN junction with overlapping states, so quantum barrier transfer is possible. That makes sub-threshold current possible in the low-forward-bias regime, which in turn makes ultra-low-bias switching possible for the wake circuit. Because the device is also scanned through a peak-to-valley window, a negative differential response is possible as well. By contrast, the conventional junction lacks the structural conditions for the same transfer mode, so it cannot deliver the same low-bias switching task in this case.  
+
+## Check  
+C1  OK - the tunnel junction can support quantum barrier transfer  
+C2  OK - the tunnel junction is classified as tunneling-dominant  
+C3  OK - the tunnel junction can deliver sub-threshold current  
+C4  OK - the tunnel junction can show negative differential response  
+C5  OK - the tunnel junction can perform ultra-low-bias switching  
+C6  OK - the tunnel junction can serve the leak-alarm wake circuit  
+C7  OK - the conventional junction cannot support the same quantum barrier transfer  
+C8  OK - the conventional junction cannot deliver sub-threshold current in this regime  
+C9  OK - the conventional junction cannot show the tunnel-style negative differential response  
+C10 OK - the conventional junction cannot perform ultra-low-bias switching here  
+C11 OK - the conventional junction cannot serve the leak-alarm wake circuit in this case  

package/examples/output/{act-yeast-self-reproduction.txt → act-yeast-self-reproduction.md}

@@ -1,23 +1,29 @@
-ACT yeast self-reproduction
+# act-yeast-self-reproduction  
 
-Answer
-YES for the viable starter culture.
-NO for accurate self-reproduction in the non-digital contrast lineage.
+## Source files  
 
-Reason Why
-The starter genome is treated as a replicator storing digital hereditary information, while the cell machinery is treated as the vehicle that enables metabolism and copying support. Under no-design laws, digital information makes accurate genome copying possible. Because the replicator is accurate and paired with a vehicle, the whole starter cell qualifies as a self-reproducer. With a variation source and a selection environment, natural selection also becomes possible. By contrast, the non-digital lineage cannot support accurate genome copying under the same no-design-laws assumption, so it cannot sustain the same accurate self-reproduction or natural-selection story.
+- [N3 rules](../act-yeast-self-reproduction.n3)  
 
-Check
-C1  OK - no-design laws are assumed
-C2  OK - digital information is physically instantiated for the viable lineage
-C3  OK - a viable replicator is present
-C4  OK - a viable vehicle is present
-C5  OK - accurate genome copying is possible for the viable lineage
-C6  OK - the viable lineage has a replicator-plus-vehicle architecture
-C7  OK - the starter cell qualifies as a self-reproducer
-C8  OK - heritable variation is possible for the viable lineage
-C9  OK - the viable starter culture can support a natural-selection lineage
-C10 OK - the fitter viable variant is selected in the fermenter
-C11 OK - the non-digital contrast genome cannot be copied accurately under no-design laws
-C12 OK - the non-digital contrast cell cannot achieve accurate self-reproduction
-C13 OK - the non-digital contrast cell cannot support the same natural-selection lineage
+ACT yeast self-reproduction  
+
+## Answer  
+YES for the viable starter culture.  
+NO for accurate self-reproduction in the non-digital contrast lineage.  
+
+## Reason Why  
+The starter genome is treated as a replicator storing digital hereditary information, while the cell machinery is treated as the vehicle that enables metabolism and copying support. Under no-design laws, digital information makes accurate genome copying possible. Because the replicator is accurate and paired with a vehicle, the whole starter cell qualifies as a self-reproducer. With a variation source and a selection environment, natural selection also becomes possible. By contrast, the non-digital lineage cannot support accurate genome copying under the same no-design-laws assumption, so it cannot sustain the same accurate self-reproduction or natural-selection story.  
+
+## Check  
+C1  OK - no-design laws are assumed  
+C2  OK - digital information is physically instantiated for the viable lineage  
+C3  OK - a viable replicator is present  
+C4  OK - a viable vehicle is present  
+C5  OK - accurate genome copying is possible for the viable lineage  
+C6  OK - the viable lineage has a replicator-plus-vehicle architecture  
+C7  OK - the starter cell qualifies as a self-reproducer  
+C8  OK - heritable variation is possible for the viable lineage  
+C9  OK - the viable starter culture can support a natural-selection lineage  
+C10 OK - the fitter viable variant is selected in the fermenter  
+C11 OK - the non-digital contrast genome cannot be copied accurately under no-design laws  
+C12 OK - the non-digital contrast cell cannot achieve accurate self-reproduction  
+C13 OK - the non-digital contrast cell cannot support the same natural-selection lineage  

package/examples/output/annotation.md

@@ -0,0 +1,7 @@
+# annotation  
+
+## Source files  
+
+- [N3 rules](../annotation.n3)  
+- [Input TriG](../input/annotation.trig)  
+

package/examples/output/auroracare.md

@@ -0,0 +1,154 @@
+# auroracare  
+
+## Source files  
+
+- [N3 rules](../auroracare.n3)  
+
+AuroraCare — Purpose-based Medical Data Exchange  
+
+## A – Primary care visit  
+Clinician in the patient's care team accessing the patient summary for primary care management.  
+
+## Answer  
+PERMIT  
+
+## Reason Why  
+Permitted: clinician in the patient's care team, and the primary-care policy matched.  
+
+## Check  
+C1 SKIPPED - not a prohibited purpose  
+C2 OK - clinician  
+C3 OK - care-team linked  
+C4 SKIPPED  
+C5 OK - operator=isAnyOf, allowed=["https://example.org/health#PATIENT_SUMMARY","https://example.org/health#LAB_RESULTS"], requested=["https://example.org/health#PATIENT_SUMMARY"]  
+C6 SKIPPED - no prohibition matched  
+C7 OK - trace shows matching permission  
+C8 SKIPPED - no matched policy or no duties  
+C9 SKIPPED - policy has no environment constraint  
+C10 INFO - matched policy: urn:policy:primary-care-001  
+
+## B – Quality improvement (in scope)  
+QI analyst using lab results + summary in a secure environment.  
+
+## Answer  
+PERMIT  
+
+## Reason Why  
+Permitted: ODRL/DPV policy matched for secondary use.  
+
+## Check  
+C1 SKIPPED - not a prohibited purpose  
+C2 SKIPPED  
+C3 SKIPPED  
+C4 OK - opt-in present and policy matched  
+C5 OK - operator=isAllOf, allowed=["https://example.org/health#LAB_RESULTS","https://example.org/health#PATIENT_SUMMARY"], requested=["https://example.org/health#LAB_RESULTS","https://example.org/health#PATIENT_SUMMARY"]  
+C6 SKIPPED - no prohibition matched  
+C7 OK - trace shows matching permission  
+C8 INFO - duties attached: duty:https://w3id.org/dpv/legal/eu/ehds#requireConsent, duty:https://w3id.org/dpv/legal/eu/ehds#noExfiltration  
+C9 OK - operator=eq, allowed="secure_env", requested="secure_env"  
+C10 INFO - matched policy: urn:policy:qi-2025-aurora  
+
+## C – Quality improvement (out of scope)  
+QI analyst with only lab results; policy expects labs + summary.  
+
+## Answer  
+DENY  
+
+## Reason Why  
+Denied: no policy matched (purpose, environment, TOMs, or categories out of scope).  
+
+## Check  
+C1 SKIPPED - not a prohibited purpose  
+C2 SKIPPED  
+C3 SKIPPED  
+C4 OK - denied because opt-in missing or no policy match  
+C5 SKIPPED  
+C6 SKIPPED - no prohibition matched  
+C7 SKIPPED  
+C8 SKIPPED - no matched policy or no duties  
+C9 SKIPPED  
+C10 SKIPPED - no matched policy  
+
+## D – Insurance management  
+Insurance bot attempting to use health data for insurance management (prohibited purpose).  
+
+## Answer  
+DENY  
+
+## Reason Why  
+Denied: the requested purpose (insurance management) is prohibited by policy.  
+
+## Check  
+C1 OK - denied prohibited purpose  
+C2 SKIPPED  
+C3 SKIPPED  
+C4 SKIPPED  
+C5 SKIPPED  
+C6 OK - denied due to prohibition  
+C7 SKIPPED  
+C8 SKIPPED - no matched policy or no duties  
+C9 SKIPPED  
+C10 SKIPPED - no matched policy  
+
+## E – GP checks labs  
+GP for the same patient checking lab results via the API gateway.  
+
+## Answer  
+PERMIT  
+
+## Reason Why  
+Permitted: clinician in the patient's care team, and the primary-care policy matched.  
+
+## Check  
+C1 SKIPPED - not a prohibited purpose  
+C2 OK - clinician  
+C3 OK - care-team linked  
+C4 SKIPPED  
+C5 OK - operator=isAnyOf, allowed=["https://example.org/health#PATIENT_SUMMARY","https://example.org/health#LAB_RESULTS"], requested=["https://example.org/health#LAB_RESULTS"]  
+C6 SKIPPED - no prohibition matched  
+C7 OK - trace shows matching permission  
+C8 SKIPPED - no matched policy or no duties  
+C9 SKIPPED - policy has no environment constraint  
+C10 INFO - matched policy: urn:policy:primary-care-001  
+
+## F – Research on anonymised dataset  
+Researcher using anonymised labs + summary in a secure environment, with opt-in.  
+
+## Answer  
+PERMIT  
+
+## Reason Why  
+Permitted: subject opted in and an ODRL/DPV policy matched (anonymised dataset in secure environment).  
+
+## Check  
+C1 SKIPPED - not a prohibited purpose  
+C2 SKIPPED  
+C3 SKIPPED  
+C4 OK - opt-in present and policy matched  
+C5 OK - operator=isAnyOf, allowed=["https://example.org/health#LAB_RESULTS","https://example.org/health#PATIENT_SUMMARY","https://example.org/health#IMAGING_REPORT"], requested=["https://example.org/health#PATIENT_SUMMARY","https://example.org/health#LAB_RESULTS"]  
+C6 SKIPPED - no prohibition matched  
+C7 OK - trace shows matching permission  
+C8 INFO - duties attached: duty:https://w3id.org/dpv/legal/eu/ehds#annualOutcomeReport, duty:https://w3id.org/dpv/legal/eu/ehds#noReidentification, duty:https://w3id.org/dpv/legal/eu/ehds#noExfiltration  
+C9 OK - operator=eq, allowed="secure_env", requested="secure_env"  
+C10 INFO - matched policy: urn:policy:research-aurora-diabetes  
+
+## G – AI training (opt-out)  
+Data user wants to train AI, but the subject opted out of AI training.  
+
+## Answer  
+DENY  
+
+## Reason Why  
+Denied: you opted out of your data being used to train AI systems.  
+
+## Check  
+C1 SKIPPED - not a prohibited purpose  
+C2 SKIPPED  
+C3 SKIPPED  
+C4 OK - denied because opt-in missing or no policy match  
+C5 SKIPPED  
+C6 SKIPPED - no prohibition matched  
+C7 SKIPPED  
+C8 SKIPPED - no matched policy or no duties  
+C9 SKIPPED  
+C10 SKIPPED - no matched policy  

package/examples/output/backward-recursion.md

@@ -0,0 +1,11 @@
+# backward-recursion  
+
+## Source files  
+
+- [N3 rules](../backward-recursion.n3)  
+- [Input TriG](../input/backward-recursion.trig)  
+
+@prefix : <urn:example#> .  
+
+:a :reaches :b .  
+:a :reaches :c .