[tyh0123]

This carries forward @tyh0123's Josephson junction work from #152. It's rebased on current development, conflicts are resolved, and stray files are removed.

What it adds

This adds a new JosephsonJunction lumped element (Source/FieldSolver/LumpedElement/), which acts as a nonlinear inductor on grid edges:

• Supercurrent: on every edge where the critical current is nonzero, it adds a supercurrent density J_J = Ic·sin(φ)/A.
• Phase: the phase follows dφ/dt = (2e/ħ)·V, with V = E_edge·edge_length. It's advanced with leapfrog: a -dt/2 initialization push, then dt each step.
• Current accumulation: J is persistent state in this solver, so each step the junction swaps its previous contribution for the new one instead of adding on top. This fixes the accumulation bug in the last commit of Added JJ function #152, and it works alongside London or inductor current on the same edge.
• Full RCSJ model: the junction element supplies only the supercurrent. For the resistor and capacitor parts, use the existing macroscopic.lumped_resistor_* / lumped_capacitor_* inputs (implement lumped capacitor and resistor #141) on the same edges.

Inputs

algo.use_josephson_junction = 1
josephson.Ic_x_function(x,y,z) = "..."   # critical current [A]; nonzero marks junction edges
josephson.Ic_y_function(x,y,z) = "..."
josephson.Ic_z_function(x,y,z) = "..."

Diagnostics: josephson_phi_{x,y,z} and josephson_Ic_{x,y,z} are available as plotfile fields.

Checkpoint/restart: φ and the stored supercurrent are written to the checkpoint and read back on restart. Without this, φ would silently reset to 0 while the fields were restored. The junction is also included in the existing London and inductor handling of J in checkpoints, current setup and Evolve.

Changes from #152

• Merged current development, including implement lumped capacitor and resistor #141 (lumped R/C), Time varying hbias #158 (time-varying Hbias), fix compilation issues for LLG and non-LLG #161 and fix soft source double counting introduced with time-varying Hbias PR #162.
• Lumped R/C code: Added JJ function #152 contained its own copy of the lumped R/C implementation. MacroscopicProperties.H/.cpp and MacroscopicEvolveE.cpp now use upstream's version unchanged; the only differences were cosmetic.
• Setup order in WarpX::InitData: this keeps upstream's ordering, london → inductor → Josephson junction → diagnostics. The lumped elements still set up their data before diagnostics read it, and a restart calls JosephsonJunction::ReadCheckpoint right after InitData.
• Removed 5 stray .orig patch leftovers, about 2,900 lines.
• Reverted the local AMREX_HOME path change in GNUmakefile.

Testing

• Affected sources compile (3D, CPU, no MPI, LLG on)
• Junction example from a fresh start
• Junction example restarted from a checkpoint; φ continues smoothly across the restart
• Existing lumped inductor, R/C and London tests unchanged