Add per-page References sections in Karen-style bibliographic format

Match the SPIDER-docs convention: keep inline author-year hyperlinks in
prose, then close each cited page with a "## References" list of full
bibliographic entries (`Authors, *Title*, **Journal**, volume, pages.`).

Apply to ten pages: energy_diagnostics, heat_transport, mixing_length,
model, pressure_eos, spider_comparison, two_phase_flow (rename existing
"Where to read more" sections), and add new sections to installation,
proteus_coupling (How-to), and data.

Page ranges use "to" instead of dashes per the no-em/en-dash rule.

Author: timlichtenberg

docs/Explanations/energy_diagnostics.md

@@ -125,3 +125,7 @@ Cumulative `E_residual_cons_frac` of more than ~5 % over a multi-Myr run, or `so
 python tools/plot_energy_balance.py output/<run_dir> --label <run_label>
 # writes output_files/energy_balance/<label>_balance.pdf and _powers.pdf
 ```
+
+## References
+
+- [Bower et al. (2018)](https://scixplorer.org/abs/2018PEPI..274...49B/abstract). *Numerical solution of a non-linear conservation law applicable to the interior dynamics of partially molten planets*. **Physics of the Earth and Planetary Interiors**, 274, 49 to 62.

docs/Explanations/heat_transport.md

@@ -154,3 +154,8 @@ Per-staggered-node heating is in `heating` (sum of the two contributions); per-c
 ![Heat-flux decomposition](../figures/vv/fig_02_flux_decomposition.png)
 
 **Figure 2.** (a) Magnitude of the four heat-flux components $F_\text{cond}$, $F_\text{conv}$, $F_\text{grav}$, $F_\text{mix}$ and their sum on an 80-cell Earth mesh, evaluated at a fully-mushy state where the entropy on each cell is the midpoint of the local solidus and liquidus values plus a small surface-ward gradient. Open triangles mark cells where the signed flux is negative. The four components reconstruct $F_\text{tot}$ to floating-point round-off ($\max|F_\text{tot}-\sum F_i|/|F_\text{tot}| < 10^{-15}$). (b) Internal volumetric heating sources $H_\text{radio}$, $H_\text{tidal}$ at the staggered nodes for the same state, with the bundled radionuclide cocktail at $t=0$.
+
+## References
+
+- [Abe (1993)](https://scixplorer.org/abs/1993GMS....74...41A/abstract). *Thermal evolution and chemical differentiation of the terrestrial magma ocean*. **Geophysical Monograph 74**, American Geophysical Union, 41 to 54.
+- [Bower et al. (2018)](https://scixplorer.org/abs/2018PEPI..274...49B/abstract). *Numerical solution of a non-linear conservation law applicable to the interior dynamics of partially molten planets*. **Physics of the Earth and Planetary Interiors**, 274, 49 to 62.

docs/Explanations/mixing_length.md

@@ -164,16 +164,16 @@ The version of MLT in Aragog inherits five concrete choices that distinguish it
   Aragog reports $F_\mathrm{conv}$ separately from the conduction, gravitational-separation, and chemical-mixing fluxes, with reconstruction of the total to floating-point round-off (Figure 2 of [Heat transport](heat_transport.md)).
   This component-wise decomposition is not natural in a BLT formulation, where the single closed-form $F_\mathrm{surf}$ is the only flux available for diagnostics.
 
-## Where to read more
-
-- [Abe (1993)](https://scixplorer.org/abs/1993GMS....74...41A/abstract). *Thermal evolution and chemical differentiation of the terrestrial magma ocean*. Geophysical Monograph 74, American Geophysical Union, pp. 41-54. The two-regime MLT form Aragog and SPIDER both follow.
-- Abe, Y. (1995). *Basic equations for evolution of partially molten mantle and core*. In Yukutake, T. (ed.), *The Earth's Central Part: Its Structure and Dynamics*, Terra Sci. Pub. Com., Tokyo, pp. 215-230. Source for $\mathrm{Re}_\mathrm{crit} = 9/8$ via the viscous-inviscid asymptotic match.
-- [Abe (1997)](https://scixplorer.org/abs/1997PEPI..100...27A/abstract). *Thermal and chemical evolution of the terrestrial magma ocean*. PEPI 100, 27.
-- [Bower et al. (2018)](https://scixplorer.org/abs/2018PEPI..274...49B/abstract). *Numerical solution of a non-linear conservation law applicable to the interior dynamics of partially molten planets*. PEPI 274, 49. The SPIDER paper; the entropy-form mantle equation Aragog inherits.
-- [Elkins-Tanton (2008)](https://scixplorer.org/abs/2008E%26PSL.271..181E/abstract). *Linked magma ocean solidification and atmospheric growth for Earth and Mars*. EPSL 271, 181. A representative BLT magma-ocean evolution coupled to a grey atmosphere.
-- [Hamano et al. (2013)](https://scixplorer.org/abs/2013Natur.497..607H/abstract). *Emergence of two types of terrestrial planet on solidification of magma ocean*. Nature 497, 607.
-- [Lichtenberg et al. (2021)](https://scixplorer.org/abs/2021JGRE..12606711L/abstract). *Vertically resolved magma ocean-protoatmosphere evolution*. JGR Planets 126, e06711. SPIDER + atmosphere coupling that Aragog now replaces inside PROTEUS.
-- [Schaefer et al. (2016)](https://scixplorer.org/abs/2016ApJ...829...63S/abstract). *Predictions of the atmospheric composition of GJ 1132b*. ApJ 829, 63. A representative BLT magma-ocean coupled to atmospheric photochemistry and escape.
-- [Solomatov (2007)](https://scixplorer.org/abs/2007evea.book...91S/abstract). *Magma oceans and primordial mantle differentiation*. In *Evolution of the Earth*, Treatise on Geophysics 9, 91. Review of the Nu-Ra scalings BLT relies on.
-- [Solomatov & Stevenson (1993)](https://scixplorer.org/abs/1993JGR....98.5375S/abstract). *Suspension in convective layers and style of differentiation of a terrestrial magma ocean*. JGR 98, 5375.
-- [Vitense (1953)](https://scixplorer.org/abs/1953ZA.....32..135V/abstract). *Die Wasserstoffkonvektionszone der Sonne*. Zeitschrift für Astrophysik 32, 135. Origin of the inviscid free-fall MLT velocity scaling that magma-ocean MLT inherits.
+## References
+
+- [Abe (1993)](https://scixplorer.org/abs/1993GMS....74...41A/abstract). *Thermal evolution and chemical differentiation of the terrestrial magma ocean*. **Geophysical Monograph 74**, AGU, 41 to 54.
+- Abe, Y. (1995). *Basic equations for evolution of partially molten mantle and core*. In Yukutake, T. (ed.), *The Earth's Central Part: Its Structure and Dynamics*, Terra Sci. Pub. Com., Tokyo, 215 to 230.
+- [Abe (1997)](https://scixplorer.org/abs/1997PEPI..100...27A/abstract). *Thermal and chemical evolution of the terrestrial magma ocean*. **Physics of the Earth and Planetary Interiors**, 100, 27 to 39.
+- [Bower et al. (2018)](https://scixplorer.org/abs/2018PEPI..274...49B/abstract). *Numerical solution of a non-linear conservation law applicable to the interior dynamics of partially molten planets*. **Physics of the Earth and Planetary Interiors**, 274, 49 to 62.
+- [Elkins-Tanton (2008)](https://scixplorer.org/abs/2008E%26PSL.271..181E/abstract). *Linked magma ocean solidification and atmospheric growth for Earth and Mars*. **Earth and Planetary Science Letters**, 271, 181 to 191.
+- [Hamano et al. (2013)](https://scixplorer.org/abs/2013Natur.497..607H/abstract). *Emergence of two types of terrestrial planet on solidification of magma ocean*. **Nature**, 497, 607 to 610.
+- [Lichtenberg et al. (2021)](https://scixplorer.org/abs/2021JGRE..12606711L/abstract). *Vertically resolved magma ocean-protoatmosphere evolution: H$_2$, H$_2$O, CO$_2$, CH$_4$, CO, O$_2$, and N$_2$ as primary absorbers*. **Journal of Geophysical Research: Planets**, 126, e06711.
+- [Schaefer et al. (2016)](https://scixplorer.org/abs/2016ApJ...829...63S/abstract). *Predictions of the atmospheric composition of GJ 1132b*. **The Astrophysical Journal**, 829, 63.
+- [Solomatov (2007)](https://scixplorer.org/abs/2007evea.book...91S/abstract). *Magma oceans and primordial mantle differentiation*. In *Evolution of the Earth*, **Treatise on Geophysics**, 9, 91 to 119.
+- [Solomatov & Stevenson (1993)](https://scixplorer.org/abs/1993JGR....98.5375S/abstract). *Suspension in convective layers and style of differentiation of a terrestrial magma ocean*. **Journal of Geophysical Research**, 98, 5375 to 5390.
+- [Vitense (1953)](https://scixplorer.org/abs/1953ZA.....32..135V/abstract). *Die Wasserstoffkonvektionszone der Sonne*. **Zeitschrift für Astrophysik**, 32, 135 to 164.

docs/Explanations/model.md

@@ -258,3 +258,7 @@ The formulation maps to the following source modules:
 | Diagnostic helpers (rheological front, global $\phi$) | `aragog.output.diagnostics` |
 
 For the package layout in detail, see [Code architecture](code_architecture.md). For the public API, see the [API reference](../Reference/api/index.md).
+
+## References
+
+- [Abe (1993)](https://scixplorer.org/abs/1993GMS....74...41A/abstract). *Thermal evolution and chemical differentiation of the terrestrial magma ocean*. **Geophysical Monograph 74**, American Geophysical Union, 41 to 54.

docs/Explanations/pressure_eos.md

@@ -139,3 +139,7 @@ For the user-defined path (`eos_method = 2`) the cumulative mass is built from t
 | Constant-properties analytical mode | `1` (suffices; the analytical path bypasses the table lookups) |
 
 For a fuller treatment of when PALEOS-driven structures matter and how the standalone vs PROTEUS-coupled paths share the same numerical core, see [Standalone usage](../How-to/usage-paths.md) and [Coupling Aragog to PROTEUS](../How-to/proteus_coupling.md).
+
+## References
+
+- [Attia et al. (2026)](https://scixplorer.org/abs/2026arXiv260503741A/abstract). *PALEOS: Multiphase Equations of State and Mass-Radius Relations for Exoplanet Interiors*. Submitted to **A&A**, arXiv:2605.03741.

docs/Explanations/spider_comparison.md

@@ -90,3 +90,10 @@ SPIDER writes one JSON file per output time via cJSON (`monitor.c`); Aragog writ
 The downstream PROTEUS plotting and analysis tooling consumes NetCDF.
 
 For the configuration details that map between the two codes, see [Configuration](../How-to/configuration.md) and [Standalone vs PROTEUS-integrated](../How-to/usage-paths.md).
+
+## References
+
+- [Attia et al. (2026)](https://scixplorer.org/abs/2026arXiv260503741A/abstract). *PALEOS: Multiphase Equations of State and Mass-Radius Relations for Exoplanet Interiors*. Submitted to **A&A**, arXiv:2605.03741.
+- [Bower et al. (2018)](https://scixplorer.org/abs/2018PEPI..274...49B/abstract). *Numerical solution of a non-linear conservation law applicable to the interior dynamics of partially molten planets*. **Physics of the Earth and Planetary Interiors**, 274, 49 to 62.
+- [Ruedas (2017)](https://scixplorer.org/abs/2017GGG....18.3530R/abstract). *Radioactive heat production of six geologically important nuclides*. **Geochemistry, Geophysics, Geosystems**, 18, 3530 to 3541.
+- [Wolf & Bower (2018)](https://scixplorer.org/abs/2018PEPI..278...59W/abstract). *An equation of state for high pressure-temperature liquids (RTpress) with application to MgSiO3 melt*. **Physics of the Earth and Planetary Interiors**, 278, 59 to 74.

docs/Explanations/two_phase_flow.md

@@ -128,21 +128,21 @@ In that window:
 In a coupled atmosphere-interior simulation, this is the regime where atmospheric H$_2$O outgassing, surface volatile budgets, and the timing of solidification are decided.
 The one-phase formulation can give the right qualitative answer but will miss the resolved time-dependence and the radial structure that controls the coupling to the atmosphere.
 
-## Where to read more
-
-- [Bower et al. (2018)](https://scixplorer.org/abs/2018PEPI..274...49B/abstract). *Numerical solution of a non-linear conservation law applicable to the interior dynamics of partially molten planets*. PEPI 274, 49.
-  The two-phase formulation Aragog inherits, with full derivations of $j_\mathrm{grav}$, $F_\mathrm{mix}$, and the lever-rule blending.
-- [Abe (1993)](https://scixplorer.org/abs/1993GMS....74...41A/abstract). *Thermal evolution and chemical differentiation of the terrestrial magma ocean*. AGU Geophysical Monograph Series 74, 41.
-  The original two-phase magma-ocean formulation.
-- [Sasaki & Nakazawa (1986)](https://scixplorer.org/abs/1986JGR....91.9231S/abstract). *Metal-silicate fractionation in the growing Earth: Energy source for the terrestrial magma ocean*. JGR 91, 9231.
-  Stokes settling velocity of MLT convective parcels (the viscous-regime velocity scale of [Bower et al. (2018)](https://scixplorer.org/abs/2018PEPI..274...49B/abstract) Eq. 5a, used in [Mixing-length theory](mixing_length.md)).
-- [Costa et al. (2009)](https://scixplorer.org/abs/2009GGG....10.3010C/abstract). *A model for the rheology of particle-bearing suspensions and partially molten rocks*. G$^3$ 10, Q03010.
-  Source for the rheological-transition viscosity blend that Aragog uses.
-- [Solomatov & Stevenson (1993)](https://scixplorer.org/abs/1993JGR....98.5375S/abstract). *Suspension in convective layers and style of differentiation of a terrestrial magma ocean*. JGR 98, 5375.
-  Two-phase fluid-dynamical scaling for crystal suspension and settling.
-- Rumpf, H.C.H., and Gupte, A.R. (1971). *Einflüsse der Porosität und Korngrößenverteilung im Widerstandsgesetz der Porenströmung*. Chem. Ing. Tech. 43, 367. Permeability fit for the intermediate-$\phi$ branch.
-- Abe, Y. (1995). *Basic equations for evolution of partially molten mantle and core*. In Yukutake, T. (ed.), *The Earth's Central Part: Its Structure and Dynamics*, Terra Sci. Pub. Com., Tokyo, pp. 215-230. Source for the consolidated three-regime $\zeta_\mathrm{grav}(\phi)$ formulation cited in [Bower et al. (2018)](https://scixplorer.org/abs/2018PEPI..274...49B/abstract) footnote 3.
+## See also
 
 For the algebraic forms of the four heat-flux components Aragog assembles, see [Heat transport](heat_transport.md).
 For the closure that determines $\kappa_h$ in the convective flux, see [Mixing-length theory](mixing_length.md).
 For the SPIDER cross-check, see [Aragog vs SPIDER](spider_comparison.md).
+
+## References
+
+- [Abe (1993)](https://scixplorer.org/abs/1993GMS....74...41A/abstract). *Thermal evolution and chemical differentiation of the terrestrial magma ocean*. **Geophysical Monograph 74**, AGU, 41 to 54.
+- Abe, Y. (1995). *Basic equations for evolution of partially molten mantle and core*. In Yukutake, T. (ed.), *The Earth's Central Part: Its Structure and Dynamics*, Terra Sci. Pub. Com., Tokyo, 215 to 230.
+- [Bower et al. (2018)](https://scixplorer.org/abs/2018PEPI..274...49B/abstract). *Numerical solution of a non-linear conservation law applicable to the interior dynamics of partially molten planets*. **Physics of the Earth and Planetary Interiors**, 274, 49 to 62.
+- [Costa et al. (2009)](https://scixplorer.org/abs/2009GGG....10.3010C/abstract). *A model for the rheology of particle-bearing suspensions and partially molten rocks*. **Geochemistry, Geophysics, Geosystems**, 10, Q03010.
+- [Elkins-Tanton (2008)](https://scixplorer.org/abs/2008E%26PSL.271..181E/abstract). *Linked magma ocean solidification and atmospheric growth for Earth and Mars*. **Earth and Planetary Science Letters**, 271, 181 to 191.
+- [Hamano et al. (2013)](https://scixplorer.org/abs/2013Natur.497..607H/abstract). *Emergence of two types of terrestrial planet on solidification of magma ocean*. **Nature**, 497, 607 to 610.
+- Rumpf, H.C.H., and Gupte, A.R. (1971). *Einflüsse der Porosität und Korngrößenverteilung im Widerstandsgesetz der Porenströmung*. **Chemie Ingenieur Technik**, 43, 367 to 375.
+- [Sasaki & Nakazawa (1986)](https://scixplorer.org/abs/1986JGR....91.9231S/abstract). *Metal-silicate fractionation in the growing Earth: Energy source for the terrestrial magma ocean*. **Journal of Geophysical Research**, 91, 9231 to 9238.
+- [Schaefer et al. (2016)](https://scixplorer.org/abs/2016ApJ...829...63S/abstract). *Predictions of the atmospheric composition of GJ 1132b*. **The Astrophysical Journal**, 829, 63.
+- [Solomatov & Stevenson (1993)](https://scixplorer.org/abs/1993JGR....98.5375S/abstract). *Suspension in convective layers and style of differentiation of a terrestrial magma ocean*. **Journal of Geophysical Research**, 98, 5375 to 5390.

docs/How-to/installation.md

@@ -72,3 +72,8 @@ In production runs (PROTEUS-coupled or standalone), Aragog uses the [PALEOS](htt
 For SPIDER-parity reproduction or older reference runs, Aragog also accepts the [Wolf & Bower (2018)](https://scixplorer.org/abs/2018PEPI..278...59W/abstract) RTpress liquid EOS through the `phase_solid` / `phase_liquid` config keys.
 
 For a standalone install, point the `eos_dir` argument of `EntropySolver.from_file()` at any directory containing the ten required files; the canonical file list and schema are documented in [Reference: data](../Reference/data.md).
+
+## References
+
+- [Attia et al. (2026)](https://scixplorer.org/abs/2026arXiv260503741A/abstract). *PALEOS: Multiphase Equations of State and Mass-Radius Relations for Exoplanet Interiors*. Submitted to **A&A**, arXiv:2605.03741.
+- [Wolf & Bower (2018)](https://scixplorer.org/abs/2018PEPI..278...59W/abstract). *An equation of state for high pressure-temperature liquids (RTpress) with application to MgSiO3 melt*. **Physics of the Earth and Planetary Interiors**, 278, 59 to 74.

docs/How-to/proteus_coupling.md

@@ -321,3 +321,8 @@ Uniform spacing in mass-coordinate space gives larger cells at the surface where
 - **`backend = "numpy"` at production tolerances** can trip Aragog's T_core-jump retry guard at the first dt jump. Switch to `"jax"` (or loosen tolerances explicitly, knowing this will silently drift across the rheological transition).
 
 For the why behind these, see the [Coupling to PROTEUS theory page](../Explanations/proteus_coupling.md).
+
+## References
+
+- [Bower et al. (2018)](https://scixplorer.org/abs/2018PEPI..274...49B/abstract). *Numerical solution of a non-linear conservation law applicable to the interior dynamics of partially molten planets*. **Physics of the Earth and Planetary Interiors**, 274, 49 to 62.
+- [Ruedas (2017)](https://scixplorer.org/abs/2017GGG....18.3530R/abstract). *Radioactive heat production of six geologically important nuclides*. **Geochemistry, Geophysics, Geosystems**, 18, 3530 to 3541.

docs/Reference/data.md

@@ -84,3 +84,8 @@ The relevant configuration keys are summarised here for cross-reference; the ful
 | `eos_method` | `[mesh]` | `1` = Adams-Williamson; `2` = external file |
 | `eos_file` | `[mesh]` | Path to the four-column external mesh file |
 | `surface_density`, `adiabatic_bulk_modulus`, `adams_williamson_beta`, `gravitational_acceleration`, `surface_pressure` | `[mesh]` | Adams-Williamson parameters |
+
+## References
+
+- [Attia et al. (2026)](https://scixplorer.org/abs/2026arXiv260503741A/abstract). *PALEOS: Multiphase Equations of State and Mass-Radius Relations for Exoplanet Interiors*. Submitted to **A&A**, arXiv:2605.03741.
+- [Wolf & Bower (2018)](https://scixplorer.org/abs/2018PEPI..278...59W/abstract). *An equation of state for high pressure-temperature liquids (RTpress) with application to MgSiO3 melt*. **Physics of the Earth and Planetary Interiors**, 278, 59 to 74.